4: Proteins

Each turn of an alpha helix contains how many amino acids?

3.6 amino acids

How many types of organizational levels are there in the structures of the protein and what are they?

4 types The structures are: a. Primary b. Secondary c. Tertiary d. Quaternary

2. Hydrogen bond in stabilising the tertiary structure:

Amino acid side chains containing oxygen- or nitrogen-bound hydrogen, such as in the alcohol groups of serine and threonine, can form hydrogen bonds with electron-rich atoms, such as the oxygen of a carboxyl group or carbonyl group of a peptide bond.

example of globular protein

Haemoglobin and insulin.

Which protein present in muscle is insoluble in water? A.Carotene B.Insulin C.Albumin D.Myosin

Myosin

4. Ionic interactions in stabilising the tertiary structure:

Negatively charged groups, such as the carboxylate group (- COO-) in the side chain of aspartate or glutamate, can interact with positively charged groups, such as the amino group (- NH3+) in the side chain of lysine.

Which amino acid disrupts the α-helix and what does it do?

Proline because of its secondary amino group and it inserts a kink in the chain, which then interferes with the smooth, helical structure.

Which of the following is NOT an example of secondary structure found in proteins? A) Random coil B) Hydrophobic folding C) -Helix D) -Pleated sheet

Random coil

Example of a beta sheet protein

Skin fibres and Fibroin.

Example of quarternary structure protein

hemoglobin

How are peptide bonds broken?

through hydrolysis (addition of water).

β-Bends

β-Bends are generally composed of four amino acids, one of which may be proline—the amino acid that causes a "kink" in the polypeptide chain. Glycine, the amino acid with the smallest R-group, is also frequently found in β-bends.

What type of bonding is involved in beta-bend protein?

β-Bends are stabilized by the formation of hydrogen and ionic bonds.

What does β-Bends (reverse turns, β-turns) do?

β-Bends reverse the direction of a polypeptide chain, helping it form a compact, globular shape. - They are usually found on the surface of protein molecules, and often include charged residues.

differences between alpha helix and beta sheet

- Unlike the spiral and coiled α-helix (3.6 amino acid residues), β-sheets are composed of two or more peptide chains (β-strands), or segments of polypeptide chains, which are almost fully extended. - β-sheets the hydrogen bonds are perpendicular to the polypeptide backbone. - An α-helix is a right-handed structure containing disulfide bonds while a β-pleated sheet is a left-handed structure containing hydrogen bonds. - In α-helix structure of proteins, the polypeptide chains are stabilized by intramolecular hydrogen bonding whereas β-pealed sheet structure of proteins is stabilized by intermolecular hydrogen bonding.

What are the interactions that stabilize the tertiary structures?

1. Disulfide bond 2. Hydrogen bond 3. Hydrophobic interactions 4. Ionic interactions

What are the other types of amino acids that can disrupt the α-helix?

1. Large number of charged amino acids such as histidine, lysine, arginine, aspartate and glutamate can disrupt the α- helix by forming ionic bonds. 2. Amino acids with bulky side chains such as tryptophan and, 3. Amino acids with branched chain such as valine, isoleucine can disrupt the formation of the α-helix if present in large numbers.

β-Sheet

A recurring structural pattern within proteins with a pleated appearance and involved in hydrogen bonding.

3. Hydrophobic interactions in stabilising the tertiary structure:

Amino acids with non polar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules.

Which of the following statements are true about (X) and (Y)? X) Globular Protein Y) Fibrous Protein a. These are linear condensation polymers. b. Insoluble in water. c. These proteins have three dimensional folded structure. d. These are cross linked proteins. e. Soluble in water f. These are held together by intermolecular hydrogen bonds. A. X = a,b,c: Y=d,e,f B. X = c,d,e: Y=a,b,f C.X = b, c,a: Y = c.b.f D.X =a,e,f: Y=b,c,f

B. X = c,d,e: Y=a,b,f

The destruction of the biological nature and activity of proteins by heat or chemical agent is called as: A. dehydration B. denaturation C. denitrogenation D. deamination

B. denaturation

1. Disulfide bonds in stabilising the tertiary structure:

By the covalent linkages between the sulfur-containing side chains of cysteines, are much stronger than the other types of bonds that contribute to tertiary 3d structure and also by preventing it from becoming denatured in the extracellular environment.

Which bond acts like a molecular safety pin?

Disulfide bond, as keeping parts of the polypeptide firmly attached to one another.

Domains

Domains are the fundamental functional and three-dimensional structural units of polypeptides.

What happens when a protein denatures?

During the denaturation of proteins, the secondary and tertiary structures get destroyed and only the primary structure is retained.

Fibrous proteins (structural proteins)

Fibrous protein is composed of long and narrow strands where the amino acid molecule is arranged in a repetitive manner. They are linear condensation polymers. The fibrous protein is less sensitive towards change in pH and temperature and shows insolubility in water. Fibrous protein is held together by an intermolecular hydrogen bond.

globular proteins (functional proteins)

Globular protein is round and spherical in shape in which the amino acid molecules are irregularly arranged. These have three dimensional folded structure. These are cross linked proteins. They are more sensitive than fibrous protein with a change in pH and temperature. Globular proteins show solubility in water.

What are denaturing agents?

Heat, pH extremes, organic solvents, mechanical mixing, strong acids or bases, detergents and ions of heavy metals such as lead and mercury.

The helical structure of protein is stabilized by A.Peptide bond B.Dipeptide bond C.Hydrogen bond D.Vander Waal bond

Hydrogen bond

How is the hydrophobic side chains and hydrophilic side chains placed in the tertiary structure of globular proteins?

Hydrophobic side chains are placed in the interior of the molecule while the hydrophilic side chains are placed in the surface of the molecule.

What type of bonding is involved in beta-sheet protein?

Intermolecular hydrogen bonding

What type of bonding is involved in alpha-helix protein?

Intramolecular hydrogen bonding.

The bonds in protein structure, which are not broken on denaturation, are: A.Hydrogen bonds B.Peptide bonds C.Ionic bonds D.Disulphide bond

Ionic bonds

Is denaturation reversible or irreversible?

It can be reversible under ideal conditions, when the denaturing agent is removed.

α-helix

It is a spiral structure, consisting of a tightly packed, coiled polypeptide backbone core, with the side chains of the component amino acids extending outward from the central axis to avoid interfering sterically with each other. - Hydrogen bonds are used between CO and NH groups of the main chain to stabilise only.

Which of the following amino acids has been solely regarded as a ketogenic amino acid? (A). Threonine (B). Tyrosine (C). Phenylalanine (D). Leucine

Leucine

In humans, two ketogenic amino acids are

Leucine and lysine.

Once renatured, does the protein has its original shape?

No, as proteins are once denatured, it remains permanently disordered.

Does denaturation break peptide bonds?

No, it disrupts the structures of secondary and tertiary but they are not strong enough to break the peptide bonds.

How are peptide bonds formed?

Peptide bonds are formed when the amine group of one amino acid binds with the carbonyl carbon of another amino acid

How does the subunits of quarternary structure of protein functions?

Subunits may either function independently of each other, or may work cooperatively, as in hemoglobin, in which the binding of oxygen to one subunit of the tetramer increases the affinity of the other subunits for oxygen

secondary structure of protein

The way in which the chain of amino acids of the polypeptides of a protein is folded.

How are subunits held together in quaternary structure of the proteins?

They are held together by non-covalent bonds such as hydrogen bonds, ionic bonds and hydrophobic interactions.

Types of Beta Sheets

Two types: 1) Parallel beta sheet - All bonded strands have the same N to C direction. As a result they have to be separated by long sequence stretches. The hydrogen bonds are equally distanced. 2) Antiparallel beta sheet - The beta strands run in alternating directions and therefore can be quite close on the primary sequence. The distance between successive hydrogen bonds alternates between shorter and longer.

Examples of Secondary structure of protein

alpha helix, beta pleated sheet and beta bend (beta - turn).

example of fibrous protein

keratin, collagen and fibrin.

example of alpha helix

keratin, hemoglobin and myoglobin.

Quarternary structure of protein

overall protein structure, combining 2 or more polypeptides chain.

tertiary structure of protein

protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3D structure.

Fibrous protein and globular protein are characterized by the _________ structure of the protein.

tertiary

primary structure of protein

the sequence of amino acids in a protein