دورة التدريب على البحث العلمي في الكيمياء الحيوي

بسم الله الرحمن الرحيم
والصلاة والسلام على اشرف المرسلين رحمة الله للعالمين وعلى آله وصحبه وسلم
بسم الله نبدأ التدريب على البحث العلمي فى الكيمياء الحيوية
أولا نعتذر عن التأجيل الذى حدث بسبب مشكلة فنية فى المنتدى حيث ادت الى عدم استطاعة د.صبحى السحيمي البدء بأول محاضرة امس وقد كلّف ادارة المشروع بهذا الامر اليوم وها نحن نبدأ اول محاضرة مع العلم بأن خطة التدريب كما ذكره د.صبحي من قبل هو:



برنامج تدريبى على البحث العلمى فى مجال الكيمياء الحيوية:



المحاضرةالاولى

مقدمة
20/3/2006
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المحاضرة الثانية
البروتينات والاحماض الامينيه-التركيب الكيميائى للبروتين- انواع البروتينات- الخواص الكيميائية و الفيزيائيةللبروتينات-
27/03/2006
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المحاضرة الثالثة
الطرق المختلفة فى فصل و دراسة البروتينات
02/04/2006
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المحاضرة الرابعة
الكربوهيدرات- التركيب الكيميائى للسكريات- انواع السكريات- خواص السكريات
09/04/2006
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المحاضرةالخامسة
طرق فصل و تقدير و التعرف على السكريات المختلفة عمليا فى المعمل
16/04/2006
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المحاضرة السادسة
الدهون و الاحماض الدهنية- التركيب الكيميائى للدهون- انواعالدهون- الخواص الكيميائية والفيزيائية للدهون
23/04/2006
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المحاضرة السابعة
تدريب عملى على دراسة الدهونمعمليا
30/04/2006
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المحاضرة الثامنة
الفيتامينات- التركيب الكيميائى للفيتامينات- انواعالفيتامينات- الخواص الكيميائية و الفيزيائيةللفيتامينات
طرق تقدير الفيتامينات المختلفة عمليا فىالمعمل
07/05/2006
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المحاضرة التاسعة
الانزيمات- طبيعة الانزيمات- انواع الانزيمات- اهميةالانزيمات فى التفاعلات الحيوية المختلفة- خواصالانزيمات
14/07/2006
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المحاضرةالعاشرة
طرق فصل و التعرف على الانزيمات المختلفة فىالمعمل
21/05/2006
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المحاضرة الحادية عشرة
الهرمونات- طبيعة الهرمونات- التركيب الكيميائى للهرمونات- انواع الهرمونات- وظائف الهرمونات- الخواص الكيميائيةللهرمونات
28/05/2006
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المحاضرة الثانية عشرة
طرق تقدير و دراسة بعض الهرمونات فىالمعمل
04.06.2006
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المحاضرة الثالثة عشرة
الاحماض النووية- DNA, RNA – التركيب الكيميائى للحامض النووى- خواصالحامض النووى- اهمية الحامض النووى
11/06/2006
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المحاضرة الرابعة عشرة
طرق فصل الحامض النووى DNA, RNA فى المعمل و طرق تحليل ال DNA فىالمعمل
18/06/2006
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المحاضرة الخامسة عشرة
مشروع مقترح للدراسة و التدريب
25/06/2006

المحاضرة الأولى



غرض هذا الدّرس هو تقديم بعض المفاهيم الضّروريّة كمدخل لفهم علم الكيمياء الحيوية .





إن علم الكيمياء الحيوية هو علم تطبيقى يهدف الى فهم و دراسة العلاقة بين علم الكيمياء و علم الفبزياءو علم النبات و علم الحيوان و علم الفسيولوجى و هو فى المقام الأول يهدف الى دراسة العلاقة بين تركيب و وظيفة الجزيئات الحيوية ( مثل البروتينات و الدهون و السكريات .........) على مستوى الخلية الحية .و من اهم العلوم التى تستفيد من الكيمياءالحيويّة هى العلوم التى تتصل بحياة الكائن الحى مثل علم الفسيولوجى و علم الفارماكولوجى ( علم الدواء) و الميكروبيولوجى و علوم البيئة والطبّ
و علم الكيمياء الحيوية يهتم بدراسة المركبات الحيوية التى يتكون منها الكائن الحى و التفاعلات الحيوية التى تحدث داخل خلية اى كائن حى. و من اهم الجزيئات الحيوية التى سوف نتناولها هى:

1. البروتينات و الأحماض الأمينية
2. الدهون و الأحماض الدهنية
3. الكربوهيدرات ( السكريات)
4. الأنزيمات
5. الهرمونات
6. الفيتامينات
7. الأحماض النووبة (DNA, RNA)


الكيمياء الأساسيّة للجزيئات الصّغيرة:
هناك كثرة عناصر على الأرض و تدخل في النظم الحيوية، لكنّ فقط 4 عناصر تكون 99 % من الكائنات الحيّة . هذه العناصر هي الهيدروجين (H )، الأوكسيجين (O )، النّتروجين (N ) و كربون (C )، و هذه العناصر تتميز بأنها متاحة و مناسبة.

و لابد من ذكر بعض التعريفات الكيميائية الهامة

Element
Matter composed of atoms that all have the same atomic number (protons).
العنصر
هو مادة مكوّنة من عدد من الذّرّات الّتي لها نفس العدد الذّرّيّ ( بروتونات ) .


الذّرّة

Atom
The smallest component of an element that still has properties of the element, consisting of a positively charged nucleus surrounded by a charged cloud of electrons.
"+" and "-" charges strongly attract.

أصغر مكون فىالعنصر و الّذي لديه خواصّ العنصر الّذي يتكوّن من نواة موجبة الشّحنة محاطة بسحابة إلكترونية مشحونة بشحنة سالبة .
و الشحنات الموجبة و السالبة تتجاذب بقوة .


البروتون
Proton

Particle in the nucleus with a positive charge of +1 and an atomic mass number of 1 Dalton
جسيم في النواة مشحون بشحنة موجبة + 1 و عدد الكتلة الذّرّيّة له 1 دالتن .

النّيوترون
Neutron

A non-charged nuclear particle with the same mass of the proton.

جسيم غير مشحون اى متعادلداخل النواة و كتلته نفس كتلة البروتون .



الإلكترون
Electron

Negatively charged particle (-1) with a mass 1/1837 of that of a proton.

هو جسيم المشحون بشحنة سّالبة وكتلتة 1 / 1837من كتلة البروتون .







Electrons are outside the nucleus, and determine properties of the atom. Chemical reactions involve sharing or exchanging electrons. Electrons move about the nucleus in atomic orbitals. Absorption of energy can cause an electron to move up to a higher energy level. The atom is stable when the outermost energy level of most atoms has eight electrons. Electrons can be transferred carrying energy to another molecule. The H atom can carry electrons for transferring energy. Oxygen has a strong affinity for electrons. Redox reaction transfer of electrons from one molecule (oxidized) to another (reduced). Stability can be achieved by adding, losing, or sharing electrons.


Sharing electrons leads to the formation of covalent bonds. In the table, you'll see the bonding patterns of the primary biologically important elements. Bonds contain energy, and a require energy to be broken. Bond energy (expressed as kcal/mole) is the energy required to break a bond. For example, an H-H bond requires 104 kcal/mole to break.





Bonding Patterns











element --------------------->number of covalent bonds

H ---------------------> 1





O--------------------> 2





N-------------------> 3





C ------------------->4





S ------------------->5






*Chemistry of water:



Water has a simple molecular structure. It is composed of one oxygen atom and two hydrogen atoms. Each hydrogen atom is covalently bonded to the oxygen via a shared pair of electrons. Oxygen also has two unshared pairs of electrons. Thus there are 4 pairs of electrons surrounding the oxygen atom, two pairs involved in covalent bonds with hydrogen, and two unshared pairs on the opposite side of the oxygen atom. Oxygen is an "electronegative" or electron "loving" atom compared with hydrogen.









Water is a "polar" molecule, meaning that there is an uneven distribution of electron density. Water has a partial negative charge () near the oxygen atom due the unshared pairs of electrons, and partial positive charges () near the hydrogen atoms. An electrostatic attraction between the partial positive charge near the hydrogen atoms and the partial negative charge near the oxygen results in the formation of a hydrogen bond as shown in the illustration.




The ability of ions and other molecules to dissolve in water is due to polarity. For example, in the illustration below sodium chloride is shown in its crystalline form and dissolved in water. Many other unique properties of water are due to the hydrogen bonds. For example, ice floats because hydrogen bonds hold water molecules further apart in a solid than in a liquid, where there is one less hydrogen bond per molecule. The unique physical properties, including a high heat of vaporization, strong surface tension, high specific heat, and nearly universal solvent properties of water are also due to hydrogen bonding. The hydrophobic effect or the exclusion of compounds containing carbon and hydrogen (non-polar compounds) is another unique property of water caused by the hydrogen bonds. The hydrophobic effect is particularly important in the formation of cell membranes. The best de******ion is to say that water "squeezes" non-polar molecules together.





Acids and Bases, Ionization of Water









· Acid release ( Proton) H+



· Bases accept (Proton) H+



We define the pH of a solution as the negative logarithm of the hydrogen ion concentration.
at pH 7.0, a solution is neutral
at lower pH (1-6), a solution is acidic
at higher pH (8-14), a solution is basic
#Organic molecules contain carbon






Alcohol



Hydrocarbon with hydrogen replaced by "OH".



Acid



Hydrocarbon with hydrogen replaced by a carboxyl "COOH".



COOH -> COO- + H+



Amine



Hydrocarbon with hydrogen replaced by an amine "NH2". Basic- accepts protons. NH2 + H+ -> NH3+




Phosphate



Addition of -PO4=




Amino Acid



Hydrocarbon with amino and carboxyl groups



فى إنتظار استفساراتكم وتفاعلكم

[code]
بسم الله الرحمن الرحيم


المحاضرة الثانية


البروتينات و الاحماض الامينية


Proteins


Proteins are macromolecules. They are constructed from one or more unbranched chains of amino acids; that is, they are polymers. A typical protein contains 200–300 amino acids but some are much smaller (the smallest are often called peptides) and some much larger (the largest to date is titin a protein found in skeletal and cardiac muscle; it contains 26,926 amino acids.
It is difficult to describe in a simple sentence the role of proteins. Lets say:
When there is something to do, it is a protein that does it.
Therefore proteins are:
important
numerous
very diverse
very complex,
able to perform actions and reactions under some circumstances
Some examples of proteins
Antibodies: they recognize molecules of invading organisms.
Receptors: part of the cell membrane, they recognize other proteins, or chemicals, and inform the cell... 'The Door Bell'.
Enzymes: assemble or digest.
Neurotransmittorsand some hormones: Trigger the receptors... (the finger on the door bell...)
Channels,and pores: holes in the cell membrane (with or without a gate). Usually, filter the flow.




Polypeptides


Polypeptides are chains of amino acids. Proteins are made up of one or more polypeptide molecules.The amino acids are linked covalently by peptide bonds. One end of every polypeptide, called the amino terminal or N-terminal, has a free amino group. The other end, with its free carboxyl group, is called the carboxyl terminal or C-terminal.
The sequence of amino acids in a polypeptide is dictated by the codons in the messenger RNA (mRNA) molecules from which the polypeptide was translated. The sequence of codons in the mRNA was, in turn, dictated by the sequence of codons in the DNA from which the mRNA was transcribed.
The schematic below shows the N-terminal at the upper left and the C-terminal at the lower right. Proteins are made up of one or more polypeptide molecules.






Amino Acids
Proteins are linear polymers built of monomer units called amino acids. The construction of a vast array of macromolecules from a limited number of monomer building blocks is a recurring theme in biochemistry. Protein function depends on the linear sequence of amino acids. 20 different amino acids are used to synthesize proteins. The shape and other properties of each protein are dictated by the precise sequence of amino acids in it.








Each amino acid consists of an alpha carbon atom to which is attached
a hydrogen atom
an amino group (hence "amino" acid)
a carboxyl group (-COOH). This gives up a proton and is thus an acid (hence amino "acid")
one of 20 different "R" groups. It is the structure of the R group that determines which of the 20 it is and its special properties.


























The Amino Acids


For each amino acid, both the three-letter and single-letter codes are given.


Alanine----------- Ala ----------- A ------ hydrophobic


-Arginine --------Arg ----------R--- free amino group makes it basic and hydrophilic


Asparagine -----Asn --------N ----carbohydrate can be covalently linked ("N-linked) to its -NH


Aspartic acid-----Asp --------D ----free carboxyl group makes it acidic and hydrophilic


Cysteine--------------Cys -----C ------oxidation of their sulfhydryl (-SH) groups link 2 Cys (S-S)



Glutamic acid------Glu -----E -----free carboxyl group makes it acidic and hydrophilic



Glutamine---------Gln ------Q ------moderately hydrophilic



Glycine------------Gly --------G ------so small it is amphiphilic (can exist in any surroundings)



Histidine-----------His -------H ---------basic and hydrophilic


Isoleucine----------Ile --------I ---------hydrophobic


Leucine-----------Leu -------L------hydrophobic


Lysine-------------Lys--------K-------strongly basic and hydrophilic


Methionine-------Met ------M ------hydrophobic


Phenylalanine-----Phe ------F -------very hydrophobic


Proline-----------Pro ---------P ------causes kinks in the chain


Serine-----------Ser ----------S -------carbohydrate can be covalently linked ("O-linked") to its -OH


Threonine------Thr -------T ---------carbohydrate can be covalently linked ("O-linked") to its -OH


Tryptophan------Trp -----W ------scarce in most plant proteins


Tyrosine---------Tyr ------Y -------a phosphate or sulfate group can be covalently attached to its -OH


Valine-------------Val ------V -------hydrophobic



Humans must include adequate amounts of 9 amino acids in their diet. These "essential" amino acids cannot be synthesized from other precursors. However, cysteine can partially meet the need for methionine (they both contain sulfur), and tyrosine can partially substitute for phenylalanine.


The Essential Amino Acids


Histidine
Isoleucine
Leucine
Lysine
Methionine (and/or cysteine
Phenylalanine (and/or tyrosine
Threonine
Tryptophan
Valine


Two of the essential amino acids, lysine and tryptophan, are poorly represented in most plant proteins. Thus strict vegetarians should ensure that their diet contains sufficient amounts of these two amino acids.


Peptide Bond Formation by a Condensation Reaction


The formation of a peptide bond between two amino acids is an example of a condensation reaction. Two molecules are joined together with the accompanying removal of a molecule of water




الجزء الثانى من المحاضرة الثانية
Protein structure
Protein structure is broken down into four levels:
· Primary structure: refers to the "linear" sequence of amino acids.
Proteins are large polypeptides of defined amino acid sequence. The sequence of amino acids in each protein is determined by the gene that encodes it. The gene is transcribed into a messenger RNA (mRNA) and the mRNA is translated into a protein by the ribosome
.







Primary structure is sometimes called the "covalent structure" of proteins because, with the exception of disulfide bonds (see below), all of the covalent bonding within proteins defines the primary structure. In contrast, the higher orders of proteins structure (i.e. secondary, tertiary and quartenary) involve mainly noncovalent interactions.
· Secondary structure is "local" ordered structure brought about via hydrogen bonding mainly within the peptide backbone. The most common secondary structure elements in proteins are the alpha (a) helix and the beta (b) sheet (sometime called b pleated sheet).

α- Helex

β- Sheet


Tertiary structureis the "global" folding of a single polypeptide chain. A major driving force in determining the tertiary structure of globular proteins is the hydrophobic effect. The polypeptide chain folds such that the side chains of the nonpolar amino acids are "hidden" within the structure and the side chains of the polar residues are exposed on the outer surface. Hydrogen bonding involving groups from both the peptide backbone and the side chains are important in stabilizing tertiary structure. The tertiary structure of some proteins is stabilized by disulfide bonds between cysteine residues.

· Quaternary structure involves the association of two or more polypeptide chains into a multi-subunit structure.
Quaternary structure is the stable association of multiple polypeptide chains resulting in an active unit. Not all proteins exhibit quartenary structure. Usually, each polypeptide within a multisubunit protein folds more-or-less independently into a stable tertiary structure and the folded subunits then associate with each other to form the final structure. Quaternary structures are stablized mainly by noncovalent interactions; all types of noncolvalent interactions: hydrogen bonding, van der Walls interactions and ionic bonding, are involved in the interactions between subunits. In rare instances, disulfide bonds between cysteine residues in different polypeptide chains are involved in stabilizing quaternary structure.
Protein Function
Every function in the living cell depends on proteins.
Motion and locomotion of cells and organisms depends on contractile proteins. [Examples: Muscles]
The catalysis of all biochemical reactions is done by enzymes, which contain protein.
The structure of cells, and the extracellular matrix in which they are embedded, is largely made of protein. [Examples: Collagens] (Plants and many microbes depend more on carbohydrates, e.g., cellulose, for support, but these are synthesized by enzymes.)
The transport of materials in **** fluids depends of proteins.
The receptors for hormones and other signaling molecules are proteins.
Proteins are an essential nutrient for heterotrophs.
The tran******ion factors that turn genes on and off to guide the differentiation of the cell and its later responsiveness to signals reaching it are proteins.
and many more — proteins are truly the physical basis of life.
Protein Classification
The shape of a protein determines its biological activity. A single protein may have varying structure and more than one function. Proteins have many different biological functions Proteins are classified according to their biological roles.
· Enzymatic Proteins


The most varied and most highly specialized proteins are those with catalytic activity--the enzymes. Virtually all the chemical reactions of organic biomolecules in cells are catalyzed by enzymes. Many thousands of different enzymes, each capable of catalyzing a different kind of chemical reaction, have been discovered in different organisms. Digestive enzymes hydrolyze the polymers in food.
· Transport Proteins


These proteins are involved in transporting other substances. For example, hemoglobin, the iron-containing protein of blood, tranports oxygen from the lungs to other parts of the ****. Other proteins transport molecules across cell membranes.
· Structural Proteins


Structural proteins are very important for support. Collagen and elastin provide a fibrous framework in animal connective tissues, such as tendons and ligaments. Keratin is the protein of hair, horns, feathers, quills, and other skin appendages of animals.
· Storage Proteins


These proteins store amino acids. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants store proteins in seeds.
· Hormonal Proteins


Hormonal proteins coordinate the bodily activities. Insulin, a hormone secreted by the pancreas, helps regulate the concentration of sugar in the blood.
· Receptor Proteins


Receptor proteins are built into the membrane of a nerve cell and they detect chemical signals released by other nerve cells. They are involved in the cell's response to chemical stimuli.
· Contractile Proteins


These proteins are very important in movement. Actin and myosin are responsible for the movement of muscles. Contractile proteins are responsible for the undulations of cilia and flagella, which propel many cells.
· Defensive Proteins


These proteins protect against diseases. Antibodies combat bacteria and viruses.


Types of Proteins


A protein molecule that consists of but a single polypeptide chain is said to be monomeric; proteins made up of more than one polypeptide chain, as many of the large ones are, are called oligomeric. Based upon chemical composition, proteins are divided into two major classes:
· simple proteins, which are composed of only amino acids,
and
· conjugated proteins, which are composed of amino acids and additional organic and inorganic groupings, certain of which are called prosthetic groups(prosthetic group, non-amino acid portions of certain protein molecules. The key part of the prosthetic group may be either organic (such as a vitamin) or inorganic (such as a ****l) and is usually required for biological activity, especially when the prosthetic group is complexed with an enzyme). Conjugated proteins include glycoproteins, which contain carbohydrates; lipoproteins, which contain lipids; and nucleoproteins, which contain nucleic acids.
Classified by biological function, proteins include the enzymes, which are responsible for catalyzing the thousands of chemical reactions of the living cell; keratin, elastin, and collagen, which are important types of structural, or support, proteins; hemoglobin and other gas transport proteins; ovalbumin, casein, and other nutrient molecules; antibodies, which are molecules of the immune system (see immunity); protein hormones, which regulate ****bolism; and proteins that perform mechanical work, such as actin and myosin, the contractile muscle proteins