2 amino acids and proteins lecture 2

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Principle of Biochemistry 2-Amino Acids and Proteins Course code: HFB324 Credit hours: 3 hours Dr. Siham Gritly 1 Dr. Siham Gritly

Transcript of 2 amino acids and proteins lecture 2

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Principle of Biochemistry 2-Amino Acids and Proteins

Course code: HFB324Credit hours: 3 hours

Dr. Siham Gritly

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Terms should be learned

• Protein; molecule consisting of one or more polypeptide chains

• amino acid; an amino group and a carboxylic acid group attached to an “alpha” carbon (α-C); a hydrogen and a small organic group (e.g., —H, —CH3, —CH2OH), called an R-group, are also attached to the α-C

• Amphoteric; organic substance that acts as both an acid and a base

• chiral compound; molecule that cannot be superimposed on its mirror image

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• Enantiomers; two organic compounds that are are mirror images; these compounds contain one or more chiral carbons

• L-amino acid; stereoisomeric form of amino acids found in proteins

• N-terminus; (of a protein) the free amino end• peptide bond; linkage between the amino group of

one amino acid and the carboxyl group of another amino acid

• peptide or polypeptide; a polymer chain of three or more amino acids

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• R-group; (of an amino acid) one of twenty (or more) different organic groups bonded to the alpha carbon

• Stereoisomers; molecules with the same chemical formulae; they differ only in the way the different attached groups are oriented in space

• Zwitterions; ion with a positive and a negative charge

• Chirality describes the ability of a molecule to rotate the plane of polarized light either to the right (dextrorotatory) or to the left (levorotatory

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Composition and nature of proteins;

• Proteins are complex organic compound found in animal and plant tissues.

• The protein molecules are nitrogen-containing

amino acids, in addition to carbon, oxygen, and hydrogen.

• some of which are essential in the sense that humans cannot make them internally

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Protein functions1-Structural function

• -Structural function Component of all cell membranes

• Component of cytoplasm "cytoskeleton"• Component of movement or contractile

structures, such as muscle, • Component of hair, nails horns, etc. (Keratin

is the main protein of these substances)

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Protein functions 2-Metabolic functions

• 1-enzymatic function• Most specialized proteins with catalytic

activity.

• All chemical reactions of organic biomolecules in cells are catalyzed by enzymes

• Enzymes mainly consist of proteins.

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• 2-hormones (Regulatory Proteins)• Help regulate cellular or physiological activity.

• The cellular response to many hormonal signals is often mediated by a class of GTP-binding proteins called G proteins.

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• G proteins are important signal transduction molecules in cells

• transmitting chemical signals originating from outside a cell into the inside of the cell.

• G proteins activity is regulated by factors that control their ability to bind to and hydrolyze guanosine triphosphate (GTP) to guanosine diphosphate (GDP).

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• 3-Immune function (Defense Proteins)• Defend organisms against invasion by other

species or protect them• Immunoglobulin or antibodies, are made by the

lymphocytes of vertebrates and can recognize & precipitate or neutralize invading bacteria

• Fibrinogen and thrombin are blood clotting proteins

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• 4-Acid base balance buffering agent• Buffers ; are compounds that recover or (improve) a

change in pH that occur in response to the addition of alkali or acid to the solution or; A Buffers are substances that can bind protons

• Intracellular fluids; protein have the most buffering effect due to its high concentration in the blood.

• Less concentration of protein such as albumin in blood causes osmotic pressure in blood plasma decrease and thus fluid leak out into interstitial spaces causing edema or swelling

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edema or swelling

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• Protein molecules possess basic and acidic groups (Amphoteric molecules )which act as H+ acceptors or donors respectively if H+ is added or removed.

• A solution with a high hydrogen ion concentration has a low pH and is therefore more acidic,

• whereas a solution with a low hydrogen ion concentration has a high pH and is more alkaline

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•  Protein buffer: COOH (acid) of amino acid can lose H+ (COO-)

• NH2 (amine) of amino acid can gain H+ (NH3+) (buffering effect)

Lysine structure

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• 5-transport• Bind and carry molecules or ions to organs in

the blood plasma.

• Lipoproteins in blood plasma carries lipids from the live to other organs

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• 6-Energy sources • any amounts above the needed amino acids for

synthesis of tissues are metabolized and degraded.• *The amino group of amino acid is converted to

urea in the liver and excreted in urine through urea cycle.

• *carboxylic group of amino acids are converted to glucose and enter glycolysis pathway for energy production.

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7-Nutrient and Storage Proteins• Seeds of many plants store nutrient proteins

required for the growth of the germinating seedlings.

• Ovalbumin, the major protein of egg white, and casein the major protein of milk are examples of nutrient proteins

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Denaturation of proteins

• Denaturation is the breakdown of all covalent bonds causing change in shape and thus loss of function.

• Denaturation is due to• -pH• -temperature• -salt concentration• alcohol• heavy metals

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Protein structure Each protein has a unique shape or conformation. all proteins

are composed exclusively of subunits of amino acids, which join together in long chains called polypeptides that fold or coil into

the unique shape of the functional protein

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1-Primary structure of proteinsamino acids sequences • The primary structure of a protein simply

consists of its linear sequence of amino acids; for example, "alanine-glycine-tryptophan-serine-glutamate-asparagine-glycine-lysine-…

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2-Secondary structure

• As peptide bonds are formed, aligning the amino acids, hydrogen bonds form between different amino acids in the chain.

• This bonding coils the polypeptide into the secondary structure of the protein, most commonly the alpha helix,

• The α-helix coils at every 4th amino acid.

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2-Secondary structure The α-helix coils of protein

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Pleated Proteinthe polypeptide have portions that lie parallel to each other (held by hydrogen bonds) instead of in the alpha helix, in which

the amino acids’ hydrogen bonds form a pleated structure. Fibrous proteins have significant pleated structures

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3-Tertiary Structure of protein• the side chains (the R groups) of amino acids may fold

independently into a functional unit called the domain.

• Domains are connected by the rest of the polypeptide.

• The folding of a protein into its domains is related to

the hydrophilic or hydrophobic properties of its amino acids.

• Domain formation is part of the tertiary structure or proteins. globular shape (globulin)

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Tertiary Structure of protein

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• 5 kind of bonds stabilize tertiary structure• 1-van der Waals interaction (between

neighboring atoms) Van der Waals forces include attractions and repulsions between atoms, molecules, and surfaces

• 2-H-bonds within the chains or between chains

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• 3-hydrophobic interactions (between non polar)

• 4-ionic interactions (between oppositely charged groups)

• 5-disulphide linkages, the SH groups of two neighboring cysteines form –s=s bond known as disulphide linkage. (covalent bond)

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Amino acid Cysteine disulphide linkages

composed of two cysteines linked by a disulfide bond

Amino acid Cysteine

two cysteines linked by a disulfide bond

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4-Quaternary Protein Structure the structure formed by several protein molecules (polypeptide chains), usually called protein subunits

• If two or more polypeptide chains join in aggregate, they form a quaternary structure, such as in the protein molecule, hemoglobin.

• Often quaternary proteins are complexed with a different molecule, often a mineral. Hemoglobin contains iron, for example.

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4-Quaternary Protein Structure

Haemoglobin structure

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Amino acid the building block

of proteins

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Amino AcidGeneral structure of amino acid

The carbon atom next to the carboxyl group is called the α carbon and amino acids with a side-chain bonded to this carbon

are referred to as alpha amino acids. These are the most common form found in nature.

Lysine structure

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Amino acids

• Amino acids contain Carbon,

Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur

• Amino acids have two function groups (both of which are typically in the ionized form)

• 1- NH2 Amino functional group

• 2-COOH Carboxyl functional group• Both functional groups attach to a specific carbon, the alpha α

carbon, of the carbon chain. The third bonding site of the alpha carbon is typically Hydrogen.

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• The alpha carbon will have at its fourth bonding site a side chain, or R group which gives the amino acid its unique structure and properties.

• There are 20 + different amino acids in protein. All have a common structure except for the R group.

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• Some amino acids have R groups that are polar (hydrophilic), interact with water at physiological pH (O, N)

• some R groups are nonpolar (and hydrophobic C, H),

• some have acidic side chains pKa < the physiological pH 7.4. (generally with a negative charge) and some are basic pKa > the physiological pH 7.4

• pKa acid-ionization constant or acidity constant

• measure of the strength of an acid in solution

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• Some with Amino Acids with Aliphatic R-Groups nonpolar and hydrophobic (Hydrophobicity increases with increasing number of C atoms in the hydrocarbon chain)

• Aromatic Amino Acids with benzene ring are relatively nonpolar. aromatic amino acids absorb ultraviolet light.

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• • Amino acids are joined together by a dehydration synthesis of amino/carboxyl groups forming a peptide bond.

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α-Amino Acids structure Found in ProteinsBackbone of the amino acids is red, R-groups are black reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC | info @ themedicalbiochemistrypage.org

Q

Amino Acid

Symbol Structure* pK1

(COOH)

pK2

(NH2)

pK R Grou

p

Amino Acids with Aliphatic R-Groupsnonpolar and hydrophobic (C )

Glycine Gly – G 2.4 9.8

Alanine Ala – A 2.4 9.9

Valine Val – V 2.2 9.7

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α-Amino Acids Found in ProteinsBackbone of the amino acids is red, R-groups are black

reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC | info @ themedicalbiochemistrypage.org

Leucine

Leu – L

2.3 9.7

Isoleucine

Ile – I

2.3 9.8

Non-Aromatic Amino Acids with Hydroxyl R-Groups

Serine Ser –

S 2.2 9.2 ≈13

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α-Amino Acids Found in ProteinsBackbone of the amino acids is red, R-groups are black reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC | info @

themedicalbiochemistrypage.org

Threonine Thr – T 2.1 9.1 ≈13

Amino Acids with Sulfur-Containing R-Groups

nonpolar and hydrophobic

Cysteine Cys – C 1.9 10.8 8.3

Methionine Met – M 2.1 9.3

Acidic Amino Acids and their AmidesAcidic Amino Acids and their Amides Acidic amino acids are polar and negatively

charged at physiological pH. Both acidic amino acids have a second carboxyl group hydrophilic

Aspartic Acid Asp – D 2.0 9.9 3.9

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α-Amino Acids Found in ProteinsBackbone of the amino acids is red, R-groups are black

reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC | info @ themedicalbiochemistrypage.org

Asparagine

Asn – N 2.1 8.8

Glutamic Acid

Glu – E 2.1 9.5 4.1

Glutamine Gln – Q 2.2 9.1

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α-Amino Acids Found in ProteinsBackbone of the amino acids is red, R-groups are black

reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC | info @ themedicalbiochemistrypage.org

Basic amino acids

Arginine Arg – R 1.8 9.0 12.5

Lysine Lys – K 2.2 9.2 10.8

Histidine His – H 1.8 9.2 6.0

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α-Amino Acids Found in ProteinsBackbone of the amino acids is red, R-groups are black

reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC | info @ themedicalbiochemistrypage.org

Amino Acids with Aromatic Rings cyclic side groups (benzene ring)

Phenylalanine Phe – F 2.2 9.2

Tyrosine Tyr – Y 2.2 9.1 10.1

Tryptophan Trp – W 2.4 9.4

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α-Amino Acids Found in ProteinsBackbone of the amino acids is red, R-groups are black

reference; Michael W King, PhD | ©996–2012 themedicalbiochemistrypage.org, LLC | info @ themedicalbiochemistrypage.org

Imino Acids

Proline Pro – P 2.0 10.6

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The amino acids found in proteins have a common stereochemistry Optical Properties of the Amino Acids

Isomerism

• In organic chemistry, this stereochemistry is referred to as L (for levo, meaning left).

• A tetrahedral carbon atom with 4 distinct constituents is said to be chiral

• Chirality is the ability of a molecule to rotate the plane of polarized light either to the right (dextrorotatory) or to the left (levorotatory).

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• All of the amino acids in proteins exhibit the same steric configuration as L-glyceraldehyde

• the amino group is always to the left side of the alpha carbon, Thus, the amino acids found in proteins are L-alpha amino acids

• D-amino acids are never found in proteins, although they exist in nature. D-amino acids are often found in polypetide antibiotics

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Acid-Base Properties of the Amino Acids

• The α-COOH and α-NH2 groups in amino acids are capable of ionizing (as are the acidic and basic R-groups of the amino acids). As a result of their ionizability the following ionic equilibrium reactions may be written:

• R-COOH <——> R-COO– + H+ • R-NH3

+ <——> R-NH2 + H+

• The equilibrium reactions, demonstrate that amino acids contain at least two weakly acidic groups.

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the carboxyl group is stronger acid than the amino group. At physiological pH (around 7.4) the carboxyl group will be unprotonated and the amino group will be protonated.

An amino acid with no ionizable R-group would be electrically neutral at this pH. This species is termed a zwitterion.

An amino acid in its (1) un-ionized and (2) zwitterionic forms

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• Carboxylic acid groups (−CO2H) can be deprotonated to become negative carboxylates (−CO2

− ),

• and α-amino groups (NH2−) can be protonated to become positive α-ammonium groups (+NH3−).

• •

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Amino acid and peptide linkage

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Peptide linkageamino acids are the structural units of the body protein. They are

all α amino-carboxylic acids. All amino acids join together to form Peptide link. Peptide bond is formed by condensation

reaction and broken by hydrolysis

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Peptide linkageAll peptides and polypeptides are polymers of α-

amino acids

• *A protein starts as a chain of amino acids, called a polypeptide

• *Amino acids are joined by the peptide bond, via dehydration synthesis to form the polypeptide

• *The polypeptide chain is referred to as the primary structure of the protein.

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• *The specific amino acids in the polypeptide chain will determine its configuration, or shape, and therefore, its function.

• one amino acid substitution in the bonding sequence of a polypeptide can alter the final protein's shape and ability to function

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• *Nonessential amino acids can be synthesized through a process called transamination.

• *Transamination involves the transfer of an amino acid group from 1 amino acid to a carbon skeleton to form a new amino acid.

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• Amino acids can be transaminated to form alanine from pyruvate

• *the alanine is transported to the liver as primary substrate for gluconeogenesis

• *this process known as glucose-alanine cycle

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Diseases associated with protein Sickle Cell Compared

with Normal Red Blood Cell

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• sickle-cell anemia: a hereditary form of anemia• characterized by abnormal sickle- or crescent-shaped

red blood cells. Sickled cells interfere with oxygen transport and blood flow.

• Symptoms are precipitated by dehydration and insufficient oxygen (as may occur at high altitudes) and include hemolytic anemia (red blood cells burst), fever, and severe pain in the joints and abdomen.

• gene expression: the process by which a cell converts• the genetic code into RNA and protein.

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Protein-Energy Malnutrition

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• Adult Bone Loss (Osteoporosis• Cancer• Heart disease

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Protein synthesis • *For synthesis of protein all amino acids should be

present or available at the same time (essential amino acids). Synthesis or building of body proteins controlled by genetic material found in every cell.

• *the genetic material found in the nucleus of the cell is Deoxyribose Nucleic Acid (DNA)

• *the material DNA is used for synthesis of Ribose Nucleic Acids (RNA).

• *there are different forms of RNA, such as mRNA which carries information to the cytoplasm where the protein are synthesized.

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• *DNA & RNA are composed of ribose (pentose sugar) or deoxyribose, phosphoric acid and nitrogenous base (purine and pyrimidine)

• *in cytoplasma RNA moleculs tRNA direct the amino acids to correct position with the mRNA to built peptide chain and thus formation of body proteins.

• The coming lectures the discussion will be in more details

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• This process of messenger RNA being made from a template of DNA is known as transcription.

• This process of messenger RNA directing the sequence of amino acids and synthesis of proteins is known as translation.

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Protein break down (catabolism)

• *any amounts above the needed amino acids for synthesis of tissues are metabolized.

• *amino acids have both amino group and carboxylic group. The amino group of amino acid is converted to urea in the liver and excreted in urine through urea cycle.

• *carboxylic group of amino acids are converted to glucose and enter glycolysis pathway for energy.

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Lab technique for studying protein purification, structure and function

• Proteins may be purified from other cellular components using a variety of techniques;

• such as ultracentrifugation, • precipitation, • electrophoresis, and chromatography; • Methods commonly used to study protein structure and

function include; immunohistochemistry, • site-directed mutagenesis,• nuclear magnetic resonance • mass spectrometry

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References

• Murry K. Robert, Granner K. daryl, Mayes A. peter, Rodwell W. Victor (1999). Harpers Biochemistry. Appleton and Lange , twenty fifth edition

• Heymsfield, SB.; Olafson RP.; Kutner MH. and Nixon DW. 1979. A radiographic method of quantifying protein-calorie under nutrition American Journal of Clinical Nutrition, 32: 693-702

• Chang, Raymond (2007). Chemistry, Ninth Edition. McGraw-Hill. pp. 52.

• Sareen S. Gropper, Jack L.Smithh and James L. Groff; 2007. advanced Nutrition and Human Metabolism, fifth ed. Wadsworth CENGAGE learning

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• Michael W King, PhD | © 1996–2012 themedicalbiochemistrypage.org, LLC | info @ themedicalbiochemistrypage.org

• D. Voet, J. G. Voet, Biochemistry, second edition ed., John Wiley &• Sons, New York, 1995

• Sareen Gropper, Jack Smith and James Groff, Advanced Nutrition and Human Metabolism, fifth ed. WADSWORTH

• Melvin H Williams 2010; Nutrition for Health, Fitness and Sport. 9 th ed, McGraw Hill• • Heymsfield, SB.; Baumgartner N.; Richard and Sheau-Fang P. 1999. Modern

Nutrition in Health and Disease; Shils E Maurice, Olson A. James, Shike Moshe and Ross A. Catharine eds. 9th edition

• Guyton, C. Arthur. 1985. Textbook of Medical Physiology. 6th edition, W.B. Company