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2- Proteins2- Proteins

Many Structures, Many FunctionsMany Structures, Many Functions

1.1. A polypeptide is a polymer of amino acids connected in a specific sequence A polypeptide is a polymer of amino acids connected in a specific sequence 2.2. A protein’s function depends on its specific conformationA protein’s function depends on its specific conformation

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Their functions include structural support, storage, transport of Their functions include structural support, storage, transport of other substances, intercellular signaling other substances, intercellular signaling الخلوية بين الخلوية اإلشارات بين , ,اإلشاراتmovement, and defense against microbes.movement, and defense against microbes.

Some proteins works as enzymes in the cell that regulate Some proteins works as enzymes in the cell that regulate metabolism metabolism األيضاأليض by accelerating by accelerating تسريعتسريع chemical reactions.chemical reactions.

Humans have tens of thousands of different proteins, each with Humans have tens of thousands of different proteins, each with their own structure and function.their own structure and function.

All protein polymers are constructed from All protein polymers are constructed from من من تتركب the same set of the same set of تتركب20 monomers, called amino acids.20 monomers, called amino acids.

Polymers of proteins are called polypeptides Polymers of proteins are called polypeptides عديدة عديدة ببتيدات ..ببتيدات

A protein consists of one or more polypeptides folded and coiled A protein consists of one or more polypeptides folded and coiled into a specific conformationinto a specific conformation

2-Proteins2-Proteins

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- The physical and chemical characteristics - The physical and chemical characteristics صفاتصفات of the of the RR group group determine determine تحدد the unique characteristics of a particular amino the unique characteristics of a particular amino acid.acid.

Side chain

Amino group

Carboxyl group

- They are Polymers of amino acids (constructed from 20 amino - They are Polymers of amino acids (constructed from 20 amino acids) (to form Polypeptides).acids) (to form Polypeptides).

General Formula General Formula of the Amino of the Amino Acid:Acid: CC

HH

RR

NNHH

HHCC

OOHH

OO

- The side chain RR links with بـ different compounds ترتبط

- These components include - These components include aa hydrogen atomhydrogen atom, a , a carboxyl groupcarboxyl group, an , an amino groupamino group, and a , and a variable variable متغيرةمتغيرة R R groupgroup (or side chain). (or side chain).

- Differences in R groups produce the 20 different amino acids.

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1.1. Hydrophobic:Hydrophobic: the amino acids that have hydrophobic the amino acids that have hydrophobic RR groups groups (non-polar). (non-polar).

Fig. 5.15, Page 72

Amino acids Amino acids األحماض األحماضاألمينيةاألمينية

2- 2- Hydrophilic:Hydrophilic: the amino acids that have polar the amino acids that have polar RR groups, making groups, making them hydrophilic. them hydrophilic.

3- 3- Ionized:Ionized: the amino acids with functional groups that are charged the amino acids with functional groups that are charged (ionized) at cellular pH (7). So, some (ionized) at cellular pH (7). So, some RR groups are groups are basesbases, others are , others are acidsacids..

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1.1. Hydrophobic:Hydrophobic: the amino acids that have hydrophobic the amino acids that have hydrophobic RR groups groups (non-polar). (non-polar).

Fig. 5.15, Page 72

Amino acidsAmino acids

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2- 2- Hydrophilic:Hydrophilic: the amino acids that have polar the amino acids that have polar RR groups, making groups, making them hydrophilic. them hydrophilic.

3- 3- Ionized:Ionized: the amino acids with functional groups that are charged the amino acids with functional groups that are charged (ionized) at cellular pH (7). So, some (ionized) at cellular pH (7). So, some RR groups are groups are basesbases, others are , others are acidsacids..

Fig. 5.15, Page 73

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Peptide bondsPeptide bonds

Peptide bond formed between the Peptide bond formed between the carboxyl groupcarboxyl group of one amino acid of one amino acid and the and the amino groupamino group of the other by dehydration. of the other by dehydration.

OOHHCC CCHH

RR

NNHH

HH

OO

HHCCHH

RR

NNHH

CCOOHH

OO

Peptide bond

PeptidePeptide

Page 73, Fig. 5.16Page 73, Fig. 5.16

Polypeptide (Protein)

DehydrationDehydration

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• Amino acids are joined together when a Amino acids are joined together when a dehydration reactiondehydration reaction removes a removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another. The resulting covalent bond is called a from the amino group of another. The resulting covalent bond is called a peptide bondpeptide bond. .

Fig. 5.16, Page 73Fig. 5.16, Page 73

• Repeating the process over and over Repeating the process over and over مرات مرات عدة creates a long polypeptide creates a long polypeptide عدةchain.chain.– At one end is an amino acid with a free amino group the (the N-terminus) At one end is an amino acid with a free amino group the (the N-terminus)

and at the other is an amino acid with a free carboxyl group the (the C-and at the other is an amino acid with a free carboxyl group the (the C-terminus).terminus).

• The repeated sequence (The repeated sequence (N-C-CN-C-C) is the ) is the polypeptidepolypeptide backbone. backbone.• Attached to the backbone are the various R groups.Attached to the backbone are the various R groups.• Polypeptides range in size from a few monomers to thousands.Polypeptides range in size from a few monomers to thousands.

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• The folding The folding إلتفافإلتفاف of a protein from a chain of amino of a protein from a chain of amino

acids occurs spontaneously acids occurs spontaneously ذاتياذاتيا..

• There are three levels of structure:There are three levels of structure:

primary primary أولىأولى, secondary , secondary ثانوىثانوى,, andand tertiary tertiary ثالثىثالثى structure, structure,

are used to organize the folding within a single are used to organize the folding within a single

polypeptide.polypeptide.

• QuaternaryQuaternary رباعىرباعى structure arises when two or more structure arises when two or more

polypeptides join to form a protein.polypeptides join to form a protein.

Levels of Protein StructureLevels of Protein Structure

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1.1. Primary structure:Primary structure:

It is a It is a single polypeptide single polypeptide chainchain of amino acids.of amino acids.

– Lysozyme, an enzyme that Lysozyme, an enzyme that attacks bacteria, consists of a attacks bacteria, consists of a polypeptide chain of 129 polypeptide chain of 129 amino acids.amino acids.

– A slight change A slight change طفيف طفيف تغيير in in تغييرthe primary structure can the primary structure can affect a protein’s affect a protein’s conformation and ability to conformation and ability to function.function.

Fig. 5.18, Page 75Fig. 5.18, Page 75

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• Sickle cell disease Sickle cell disease المنجليةالمنجلية: : an abnormal hemoglobin because of a single amino acid an abnormal hemoglobin because of a single amino acid

substitution substitution تغييرتغيير..– These abnormal hemoglobins crystallize, deforming These abnormal hemoglobins crystallize, deforming يُكسريُكسر the red the red

blood cells and leading to clogs blood cells and leading to clogs إنسدادإنسداد in tiny blood vessels.in tiny blood vessels.

Fig. 5.19, Page 75Fig. 5.19, Page 75

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2- The secondary structure:2- The secondary structure: Results from hydrogen bonds at regular intervals متساوية أبعاد along على

the polypeptide backbone.

A. CoilsA. Coils الحلزونى (α helix)

are typical shapes

that develop from

secondary structure

B.B. FoldsFolds (β pleated sheets)

الُمجعد Composed .الشيت

of several parallel αhelix

coils attached by H bonds

Fig. 5.20, Page 76

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An example for folds (beta pleated sheets) الُمجعد :الشيت Is the structural properties of silk because of the presence of so

many hydrogen bonds makes each silk fiber stronger than steel.

Fig. 5.21, Page 77

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• Tertiary structure:Tertiary structure:

is determined by a variety of interactions among among خاللخالل RR groups groups and between between RR groups and the polypeptide backbone groups and the polypeptide backbone.– These interactions include hydrogen bondshydrogen bonds among polar areas,

ionic bondsionic bonds between charged R groups, and hydrophobic interactions and Van der Van der Waals interactionsWaals interactions among hydrophobic R groups.

Fig. 5.22, Page 77

• While these three interactions are relatively weak, disulfidedisulfide bridgesbridges, strong covalent bonds that form between the sulfhydryl groups (SH) of cysteine monomers, stabilize the structure.

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4- The quaternary structure:4- The quaternary structure:

Results from the aggregation تجمع of two or more polypeptide chains.

A.A. CollagenCollagen is a fibrous protein of three polypeptides that are supercoiled, and function in connective tissues.

A.A. HemoglobinHemoglobin is a globular protein with two copies of two kinds of polypeptides

(2α and 2β).

Fig. 5.23, Page 78CollagenCollagen HemoglobinHemoglobin

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Fig. 5.24, Page 79Fig. 5.24, Page 79

The 4 forms of proteinThe 4 forms of protein

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• It is the change of protein’s conformation in response to إستجابة.the physical and chemical conditions لـ

• For example, alterations تغيير in pH, salt concentration, temperature, or other factors can denaturedenature يفرد a protein.– These forces break the hydrogen bonds, ionic bonds, and disulfide

bridges that maintain the protein’s complicated shape.

• Some proteins can return to their original shape again after denaturation, but others cannot.

Denaturation of proteinDenaturation of protein فرد فردالبروتينالبروتين

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Fig. 5.25, Page 79

مفرود

Denaturation of protein Denaturation of protein البروتين البروتين فرد فرد

فردفرد

إلى إعادةطبيعته

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Amino Amino acidsacids

Primary Primary structurestructure

Secondary Secondary structurestructure

Tertiary Tertiary structurestructure

QuaternaryQuaternary structurestructure

1- Hydrophobic 1- Hydrophobic InteractionInteraction ( (Van Van

der Waals der Waals interactioninteraction););

2- H bonds2- H bonds;;3- Ionic bonds3- Ionic bonds;;4- Di-sulfide 4- Di-sulfide

bridges bridges;;

Single chainSingle chain of amino acidsof amino acids

e.g. Lysozymee.g. LysozymeCoils &Coils &FoldsFolds

H bondsH bonds

e.g. silke.g. Collagene.g. Collagen

& Hemoglobin& Hemoglobin

two or more two or more polypeptide polypeptide

chainschains

PeptidesPeptides

Peptide ponds

Peptide pondsDehydration

Dehydration

Hydrophobic (Hydrophobic (non-polar R group))

Hydrophilic (Hydrophilic (polar R group))

Ionized (Ionized (charged charged functional groupsfunctional groups)

ProteinsProteinsPolypeptidesPolypeptides