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Proteins in general
Proteins are organic compounds of large molecular mass Proteins account for more than 50% of the dry weight of most cells Proteins are made up of carbon, hydrogen, oxygen and nitrogen. Sulphur may also be present

Structure of amino acids

Amino acids are the basic building blocks of proteins There are 20 naturally occurring amino acids

Each amino acid has at least one amino group ( them amphoteric(acidic and basic properties)

) and one carboxyl group (

), making

The -carbon (the rest don t have numbers) has a hydrogen atom, a carboxyl group and an amino group bonded to it The remaining bond is taken up by the R group, the side chain that differentiates the amino acids, giving it its uniqueness and properties y Neutral amino acids o They are amino acids with only oneamino group and one carboxyl group o The R group does not contain any amino groups or carboxyl groups, and contains hydrogen or hydrocarbons (can be unsaturated or saturated) only.  There are no proteins in the 20 naturally occurring proteins that have both amino and carboxyl groups present in the R group o They are neutral as the acidity of the carboxyl group is canceled out by the basicity of the amino group o Most amino acids are neutral, there are only 2 acidic and 3 basic out of the 20. Basic amino acids o Their R group has more amino groups than carboxyl groups, making them basic Acidic amino acids o Their R group has more carboxyl groups than amino groups, making them acidic Hydrophobic amino acids o Their R groups are non-polar, usually due to it being hydrocarbons (can be unsaturated or saturated) Hydrophilic amino acids

y y y

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Their R groups are polar, usually due to it being charged

Properties of amino acids

1. Solubility a. Amino acids dissolvereadily in water and other aqueous mediums to form ions (see below) b. They are insoluble in organicsolvents 2. Zwitterion formation a. When amino acids are dissolved in water/ aqueous medium, the hydrogen from the carboxyldissociates, making it negatively charged ( ) b. Whereas, the amino group attracts H+ ions (has a high affinity for them) , making it

positively-charged ( ) c. The amino acid hence becomes dipolar and is called a zwitterion (term specific to amino acids, as long as they are dipolar (no need equilibrium).) d. Zwitterions are electrically neutral in nature when the number of positive charges equals to the number of negative charges. This occurs at a specific pH (the isoelectric point) 3. Buffering capabilities a. Amino acids are amphoteric as it has both acidic and basic properties (they have at least one amino and one carboxyl group) b. Hence, they can act as buffer solutions, as they (the solution) can resist changes in pH when small amounts of acid or alkali is added. c. The ability to resist changes depends on the R group, the number of amino and carboxyl groupsthe R group has. 4. Isoelectric point a. Each amino acid has a specific pH at which it will exist in its neutral zwitterion form (electrically neutral) b. This point is the isoelectric point, where the amino acid will not be affected by an electric field c. At a pH lower (more acidic) than the isoelectric point, the excess H+ ions will be taken in by the amino and carboxyl groups. The amino group would become positively charged(assuming it s not taken in a H+ ion yet), while the carboxyl group would lose its negative charge (regain the hydrogen that it dissociated) d. At a pH higher(more basic) than the isoelectric point, the excess OH- ions will be neutralized by the amino and carboxyl groups. The amino group would lose its positive charge(lose the hydrogen it gained), while the carboxyl group would gain its negative charge (Hydrogen dissociated)

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e. Thus, in both cases, they amino acids are no longer electrically neutral and would be influenced by an electric field f. The isoelectric point is specific for each amino acid

Polypeptides Formation
Amino acids join together to form polypeptides (with the aid of ribosomes), through a condensation reaction between the amino and carboxyl group, forming a dipeptide (with a peptide bond and a water molecule The peptide bonds can be broken by hydrolysis (addition of water), with the aid of enzymes. Further reaction between the dipeptide and amino acids would lead to the formation of a polypeptide. )

Polypeptides have two ends, the N-terminal (amino end ).

) and the C-terminal (carboxyl end

The N-terminal is taken to be the start of the polypeptide and naming the sequence begins here. The order of the amino acid sequence matters, as different order results in different properties.

Bonds in protein structure

Each polypeptide has a specific 3-dimensional shape (configuration), due to the bonds formed between amino acids residues in the polypeptide chain These bonds are peptide bonds, hydrogen bonds, ionic bonds, disulphide bonds andhydrophobic interaction y Peptide bonds They are amide bonds ( ) that forms the backbone (main chain, linear sequence of amino acid residues) of the polypeptide Ionic bonds o They are weak electrostatic interactionbetween oppositely charged ions o

o o

These ions are the ionized acidic( ) and basic ( ) R groups, which are formed at certain pHs These ions are attracted to each other, forming ionic bonds

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The amino and carboxyl groups in the peptide bond are not involved in the formation of ionic bonds. I.e. only the R groups are involved o These bonds are weak (weaker than covalent bonds) in an aqueous medium, and are easily broken by changes in pH (as they lose their charge, see isoelectric point above) Disulphide bonds o They are strong covalent bonds formed by the oxidation of the SH groups of two cysteineside-chains (only cysteine has SH in its R group) o When the SH groups are in close proximity, oxidation occurs, producing a strong covalent bond (and water) that is not easily broken Hydrogen bonds o They are electrostatic attraction between an electropositive ( +)hydrogen atom and an electronegative ( -)atom (Fluorine, Oxygen, Nitrogen) in another group/ molecule o The R groups may or may not (Hydrogen in peptide bond) be involved in the formation of hydrogen bonds o These weak bonds occur frequently along the polypeptide chain, hence they play a considerably role in the shape and stability of the polypeptide, despite their lack of strength Hydrophobic interactions (Van der Waals forces) o They are non-specific attractive forces that come into play when two or more atoms are very close o They are between non-polar, hydrophobic R groups o In order to minimize exposure to the environment, these R groups causes the polypeptide chain to fold so that the maximum number of hydrophobic groups come together, shielding themselves from the aqueous environment. o

Levels of protein structure

Each protein has its own conformation (characteristic structure and organization), determined by the primary, secondary, tertiary and quaternary structure y Primary structure o It is the number, sequence and varietyof amino acids in a polypeptide chain o The only bond involved is the peptide bond o The primary structure is unique, as proteins differ in their number, sequence and variety of their constituent amino acids o This primary structure is crucial to its properties and function, and a slight change in the structure can alter the protein s properties greatly. Secondary structure o It is the localized, repetitive folding of the polypeptide chain o Hydrogen bonds between the peptide linkages of the primary structure are involved, those in the R groups aren t

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o o

Three structures are formed by the hydrogen bonds, -helix, -pleated sheets and triple helix -helix  It is an extended spiral spring, that is stabilized by the hydrogen bonds

) between the peptide linkages in the polypeptide chain

 The oxygen atom in a peptide linkage( ) is bonded to the hydrogen atom of the peptide linkage 4 amino acids away  Hence, there are 3.6 amino acids resides in one complete turn of the helix -pleated sheets  Two or more regions of the polypeptide chain lie parallel to each other, occurring in flat, zigzag sheets  The sheets are held together by intramolecular hydrogen bonds (between the

peptide linkages ) between the sheets  These sheets can run in the same direction (parallel) or in opposite directions (anti-parallel) o Triple helix  This is mainly found in collagen  Three polypeptide chains (considered quaternary structure too) of collagen are wound together into a triple helix (forming tropocollagen), with hydrogen bonds holding them together Tertiary structure o It is the folding and bending of a protein molecule into a precise, compact, globular, 3dimensional shape that is unique to the protein o This shape is held in place by the four types of intramolecular bonds under bonds in protein structure , that occurbetween the R groups (only the R groups) o It can contain secondary structures like -helix and -pleated sheets Quaternary structure o Many complex proteins consistsof more than one polypeptide chain, which interact to form the quaternary structure o It is the combination of a number of polypeptide chainsand associated non-protein groups into a large complexand functional protein molecule. o Each polypeptide chain is called a subunit, which are held together by the four types of intramolecular bonds under bonds in protein structure .

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Fibrous protein
In a fibrous protein, the secondary structure is the most pronounced (little or no tertiary structure) The polypeptide chains form long fibers or sheets that are insoluble in water. The length of two samples of the same protein may vary It has a regular, stable structure, allowing it to perform its supportive functions Examples of fibrous proteins include collagen, keratin or fibrion

Case study on Collagen

Collagen is a major component (40% of proteins in the body) of connective tissues that is made up of tropocollagen. Tropocollagen has a triple helix structure, made up of three polypeptide chains, about a 1000 amino acids in length, containing mostly glycine, proline and hydroxyproline. The sequence glycine-prolinehydroxyproline occurs frequently The three chains are stabilized by hydrogen bonds (secondary structure, excluding those on R groups) formed between the NH group on glycine residues on one chain and the CO groups of the proline in an adjacent chain y The small size of the glycine residue(R group only contains hydrogen) makes it the only residue that can fit inside the triple helix, allowing the three chains to be very closely held o This confers great tensile strength on the collagen molecule The amino acids (other than glycine), mainly proline and hydroxyproline, have large hydrophobic R groups that face the outside of the triple helix o This causes the collagen to be insoluble, and hence a good structural protein The tropocollagen winds to form microfibrils, fibrils and eventually collagen fibers. These fibers lie parallel in bundles, allowing strong covalent cross-linkages to from between the N and Cterminals o This makes collagen a good structural protein

Globular protein
In a globular protein, the tertiary structure is the most pronounced The polypeptide chains folds tightly into a spherical shape that is soluble in water, forming colloidal (evenly distributed) solutions. The length of two samples of the same protein is always identical

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It has an irregular, unstable structure. It can perform many functions, such as enzymatic and transport Examples of globular proteins include enzymes and haemoglobin

Case study on Haemoglobin

Haemoglobin is found in the bloodstream and functions in the transport of oxygen The adult haemoglobin has a quaternary structure, consisting of four separate polypeptide chains (tetramer) of two types, 2 -chains and 2 -chains (subunits) y Each subunit is arranged such that its hydrophobic amino acids residues are buried in the interior of the folded structure (tertiary structure) , while the bulk of the hydrophilic amino acid residues are on the exterior o This makes the haemoglobin soluble in water Each subunit has a protein component (globin molecule) and a non-protein component (haem group) o This makes haemoglobin a conjugated protein (functions in interaction with other chemical groups attached by covalent bonds or by weak interactions.) There are pockets in the globin molecule for the haem group, which consists of a porphyrin ring and an iron(II) ion o The Fe2+ allows the haemoglobin to transport oxygen in the red blood cell, as it forms a strong bond with one molecule of oxygen o One face of the Fe2+ is attached to an amino acid residue, while the other is accessible for oxygen binding Each haemoglobin has 4 haem groups, as it has 4 subunits o This allows one haemoglobin molecules to transport up to 4 oxygen molecules

Protein properties
1. Denaturation o It is the loss of the 3-dimension structure (determined by the secondary and tertiary structure) of the protein molecule o It is caused by the breaking of any of the four bonds in the secondary and tertiary structure, that are responsible for maintaining the structure  This leads to the protein unfolding and the properties (dependent on shape) are lost o However, the primary structure andsome disulphide bonds remain unaffected, as they are held by strong covalent bonds o Denaturation is caused by heat, changes in pH, organic solvents, chemicals and mechanical force.

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 When heating, kinetic energy is supplied to the protein molecule, causing its atoms to vibrate violently, hence breaking the hydrogen bonds and hydrophobic interactions (Not reversible)  Changes in pH causes the ionic bonds to be broken due to either the amino or carboxyl groups losing their charges (may be reversible)  Organic solvents causes the disruption of hydrophobic interactions, as they don t need to group together anymore  Chemicals cause the disruption of all four kinds of bonds. The hydrogen bonds, ionic bonds, disulphide bonds and hydrophobic interaction  Mechanical force can break weak hydrogen bonds o If denaturing conditions are mild, reversal of conditions may restore protein shape and properties (renaturation). o But under harsh denaturing conditions, the effect is permanent and irreversible 2. Solubility o The solubility depends on the natureof the R group in contact with the external environment o Having hydrophilic R groups facing the external environment (like in globular proteins), would result in the protein being soluble o Having hydrophobic R groups facing the external environment (like in fibrous proteins), would result in the protein being insoluble 3. Buffering capacity o Proteins are amphoteric, having both acidic and basic properties, due to the amino

( ) and carboxyl ( ) groups at the terminals of the polypeptide chains in a aqueous medium Hence they can resist changesin pH by accepting or donating H+ ions

Protein function
1. Homeostatic a. The soluble proteins in blood plasma can act as buffers to resist pH changes, stabilizing it 2. Enzymatic a. All cellular chemical reactions are catalyzed by specific protein enzymes to speed up the rate of reaction 3. Hormonal a. Some protein functions as hormones in the body, like insulin and glucagon 4. Transport a. Transport proteins in the plasma membrane function in the transport of certain substances into and out of the cell b. Haemoglobin transports oxygen in vertebrates

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c. Lipoproteins transports cholesterol in the blood Storage a. The protein, ferritin, stores iron in the liver b. Myoglobin stores oxygen in the skeletal muscle cells Protection a. Antibodiesare proteins that are part of the immune system b. Some proteins, like fibrinogen, are blood clotting factors that aid in the blood clotting mechanism Support/ structural a. Collagen is a component of connective tissues, cartilage, tendons and ligaments b. Keratin is present in hair, hoofs and feathers Source of energy a. Proteins act as a source of energy during extreme starvation, only after carbohydrate and fat reserves are depleted.

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