Amino Acids Proteins, and Enzymes Types of Proteins Amino Acids The Peptide Bond

Types of Proteinsوظائف البروتينات Type Examples Structural tendons, cartilage, hair, nails Contractile muscles Transport hemoglobin Storage milk Hormonal insulin, growth hormone Enzyme catalyzes reactions in cells Protection immune response

Amino Acids Building blocks of proteinsوحدات بناء البروتين Carboxylic acid groupتحوي على Amino group Side group R gives unique characteristics R side chain I H2H—C —COOH H

Description – general properties Amino acids are derivatives of carboxylic acids formed by substitution of -hydrogen for amino functional group.

Structure a-carbon

Amino Acids Building Blocks of Proteins

Amino Acids Amino acids are the structural building blocks (monomers) of proteins.وحدات أولية من الأحماض الامينية لبناء البروتينات There are twenty different kinds of amino acids used in proteins.عشرين حامض اميني في بناء البروتينات Proteins are referred to as heteropolymers due the variety of amino acids involved in their structure. البروتينات بوليمر متعدد يحتوي على أحماض امينية مختلفة التركيب

BASICS Lets start with the basics. All amino acids have a common structural unit that is built around the alpha carbon (click 1). Lets call this the “core” structure. The figure shows the core with one of the bonds on the -carbon unassigned. A group in this location is represented by the letter R (click 1). COOH C +H3N  H R R R groups are the only variable groups in the structure. Consider R the only unknown and focus on this group to learn the structures. Hence, Rule (1) is amino acids are composed of a core group and an R group. Rule (2) is the R group gives an amino acid its structural identity and, later as we will see, its unique biochemical properties.

Examples of Amino Acids H I H2N—C —COOH H glycine CH3 H alanine

Amino Acids (cont’d.) The repeating sequence of atoms along a proteins is referred to as the polypeptide backbone. Attached to this repetitive chain are the different amino acid side chains (R-groups) which are not involved in the peptide bond but which give each amino acid its unique property.

insulin chemical structure

Amino Acids (cont’d.) Amino acids, like carbohydrates, show isomerism. Proteins are only made up of amino acids which are L-isomers. D-isomer L-isomer

AA are optically active molecules and asymmetry of their mirror images is not superimposable (except in the case of glycine where the R-group is hydrogen) according new UIPAC nomenclature L- D- forms were replaced for (S)- and (R)- system

Types of Amino Acids Nonpolar R = H, CH3, alkyl groups, aromatic O Polar ll R = –CH2OH, –CH2SH, –CH2C–NH2, (polar groups with –O-, -SH, -N-) Polar/Acidic R = –CH2COOH, or -COOH Polar/ Basic R = –CH2CH2NH2

Properties of Amino Acids High melting points, over 200C More soluble in water than in ether. Larger dipole moments than simple acids or simple amines. Less acidic than most carboxylic acids, less basic than most amines. pKa = 10 pKb = 12 => Chapter 24

Complete Proteins Provide all the essential amino acids. Examples: those in meat, fish, milk, eggs. Plant proteins are generally incomplete. Vegetarians should eat many different kinds of plants, or supplement diet with milk or eggs. مصادر البروتينات الغذائية => Chapter 24

20 Common Amino Acids You should know names, structures, pKa values, 3-letter and 1-letter codes Non-polar amino acids Polar, uncharged amino acids Acidic amino acids Basic amino acids

Amino Acids (cont’d.) Amino acids are grouped according to whether their side chains are:- acidic basic uncharged polar non polar

Acidic Amino Acids Aspartic Acid asp D Acidic Polar Aspartic Acid asp                                     Acidic Polar  Aspartic Acid asp   Acidic Polar  Glutamic Acid glu Acidic Polar Acidic Amino Acids

Lysine lys  Basic Polar  Arginine arg   Basic Polar Basic Amino Acids

Neutral Polar Amino Acids Glutamine gln Neutral Polar Tyrosine  tyr   Neutral Polar Neutral Polar Amino Acids

Non Polar Amino Acids Isoleucine ile Neutral Non-polar Methionine met

Amino Acids (cont’d.) The type of side chain is very important as it affects the solubility of the amino acid. Hydrophobic features include long non-polar (uncharged) chains or complex aromatic rings. Hydrophilic features include additional carboxyl groups or amino groups not involved in peptide bonding which are ionised in solution.

Essential Amino Acids 10 amino acids not synthesized by the body arg, his, ile, leu, lys, met, phe, thr, trp, val Must obtain from the diet All in diary products 1 or more missing in grains and vegetables

Essential Amino Acids Arginine (Arg) Threonine (Thr) Lysine (Lys) Valine (Val) Phenylalanine (Phe) Tryptophan (Trp) Methionine (Met) Histidine (His) Leucine (Leu) Isoleucine (Ile) => Chapter 24

Amino Acids (cont’d.) At neutral pH’s amino acids exist in an ionised form and have both acidic and basic properties. This is because the carboxylic group donates hydrogen ions to the solution (acidic) whereas the amino group (NH2) attracts hydrogen ions from the solution.

Zwitterion Amino acid exists as a dipolar ion. -COOH loses H+, -NH2 gains H+. Actual structure depends on pH. => Chapter 24

Amino Acids as Acids and Bases Ionization of the –NH2 and the –COOH group Zwitterion has both a + and – charge Zwitterion is neutral overall + NH2–CH2–COOH H3N–CH2–COO– glycine Zwitterion of glycine

Isoelectric Point pH at which amino acids exist as the zwitterion (neutral). Depends on structure of the side chain. Acidic amino acids, isoelectric pH ~3. Basic amino acids, isoelectric pH ~9. Neutral amino acids, isoelectric pH is slightly acidic, 5-6. => Chapter 24

pH and ionization H+ OH– + + Positive ion zwitterion Negative ion + + H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–COO– Positive ion zwitterion Negative ion Low pH neutral pH High pH

Zwitterionic structure is neutral and its value of pH is called isoelectric point.

Structure and pH => Chapter 24

Structure of Peptide The peptide bond is an amide bond. Amides are very stable and neutral. => Chapter 24

Peptide Bond Formation The amino group of one molecule condenses with the acid group of another. Polypeptides usually have molecular weight less than 5000. Protein molecular weight 6000-40,000,000. => Chapter 24

Learning Check AA1 A. NH2–CH2–COOH (Glycine) CH3 | CH–OH Identify each as (1) polar or (2) nonpolar A. NH2–CH2–COOH (Glycine) CH3 | CH–OH B. NH2–CH–COOH (Serine)

Solution AA1 A.(2) NH2–CH2–COOH (Glycine) CH3 | CH–OH Identify each as (1) polar or (2) nonpolar A.(2) NH2–CH2–COOH (Glycine) CH3 | CH–OH B. (1) NH2–CH–COOH (Serine)

Amino Acids (cont’d.) Amino acids link together by covalent peptide bonds. This involves a condensation /dehydration reaction. These bonds are very strong. When this takes place the charged amino and carboxylic groups disappear.

Learning Check AA2 CH3 CH3 + H3N–CH–COOH H2N–CH2–COO– (1) (2) (1) (2) Select from the above structures A. Alanine in base. B. Alanine in acid.

Solution AA2 CH3 CH3 + H3N–CH–COOH H2N–CH2–COO– (1) (2) (1) (2) Select from the above structures (2) Alanine in base. (1) Alanine in acid.

The Peptide Bond Amide bond formed by the –COOH of an amino acid and the –NH2 of the next amino acid O CH3 + | | + | NH3–CH2–COH + H3N–CH–COO– O CH3 + | | | NH3–CH2–C – N–CH–COO– | peptide bond H

Peptides Amino acids linked by amide (peptide) bonds Gly Lys Phe Arg Ser H2N- -COOH end Peptide bonds end Glycyllysylphenylalanylarginylserine

Primary Structure of Proteins The particular sequence of amino acids that is the backbone of a peptide chain or protein Ala-Leu-Cys-Met

Learning Check AA3 What are the possible tripeptides formed from one each of leucine, glycine, and alanine?

Solution AA3 Tripeptides possible from one each of leucine, glycine, and alanine Leu-Gly-Ala Leu-Ala-Gly Ala-Leu-Gly Ala-Gly-Leu Gly-Ala-Leu Gly-Leu-Ala

Learning Check AA4 Write the three-letter abbreviations for the following tetrapeptide:

Solution AA4 Ala-Leu-Cys-Met

Hydrolysis of a Dipeptide

Learning Check P4 What are the products of the complete hydrolysis of Ala-Ser-Val?

Solution P4 The products of the complete hydrolysis of Ala-Ser-Val are alanine serine valine

Test Your Knowledge. Click to see the answer. Q: What amino acid has the shortest carbon chain in its R group? A: Glycine. It has no carbon in its R group. Q: What structural feature is common to alanine, serine and cysteine? A: All three have a single carbon in their R groups. Q: Which amino acid has the longest straight chain of carbons in its R group? A: Lysine. It has 4. Leucine and isoleucine have 4 but their chains are branched Q: What R group structural feature is common to phenylalanine, tyrosine, tryptophan, and histidine? A: All four have rings that are attached to the core via a –CH2 group Q: What structural feature is common to isoleucine and threonine A: Both have an asymmetric carbon in their R group

Peptide Bond Formation The amino group of one molecule condenses with the acid group of another. Polypeptides usually have molecular weight less than 5000. Protein molecular weight 6000-40,000,000. => Chapter 24

الأحماض للامينية المتحدة معا العدد تسعة تذكر في لتسمية عدد الأحماض الامينية المتحدة من العدد عشرة إلى العدد تسعة وتسعين تسمى بولي ببتايد إما إذا عدد الأحماض المتحدة من مائة وأكثر تسمى بروتين

Classification of Proteins Simple: hydrolyze to amino acids only. Conjugated: bonded to a nonprotein group, such as sugar, nucleic acid, or lipid. Fibrous: long, stringy filaments, insoluble in water, function as structure. Globular: folded into spherical shape, function as enzymes, hormones, or transport proteins. => Chapter 24

Levels of Protein Structure Primary: the sequence of the amino acids in the chain and the disulfide links. Secondary: structure formed by hydrogen bonding. Examples are -helix and pleated sheet. Tertiary: complete 3-D conformation. Quaternary: association of two or more peptide chains to form protein. => Chapter 24

Alpha Helix Each carbonyl oxygen can hydrogen bond with an N-H hydrogen on the next turn of the coil. => Chapter 24

Pleated Sheet Each carbonyl oxygen hydrogen bonds with an N-H hydrogen on an adjacent peptide chain. => Chapter 24

Summary of Structure => Chapter 24

Denaturation Disruption of the normal structure of a protein, such that it loses biological activity. Usually caused by heat or changes in pH. Usually irreversible. A cooked egg cannot be “uncooked.” => Chapter 24