WEEK 1: PROTEIN STRUCTURE

Question 1

What are proteins?

Answer 1

Proteins are macromolecules composed of amino acids joined together by peptide bonds.​

Question 2

How can the protein diversity of living beings be explained?

Answer 2

The genetic code specifies 20 amino acids which can be combined in many ways, hence there are a very high number of possible proteins that can be made.​

Question 3

What is the constitutional unit of proteins?

Answer 3

Amino acids

Question 4

What is the importance of proteins for living organisms?

Answer 4

Proteins are involved in catalysis of reactions as enzymes​

Proteins function as hormones i.e., messenger molecules​

Growth and maintenance of the body requires proteins for both energy and building material​

Antibodies, that protect against foreign bodies such as bacteria, are made up of proteins​

Proteins are involved in transport and storage of many substances in the body​

Energy source, when the body is unable to get what it needs from carbohydrates and lipids​

Movement of the body (actin and myosin)​

Question 5

Briefly describe the basic structure of PROTEINS.

Answer 5

Amino Acids are organic molecules that have a central carbon atom, also known as the Alpha-carbon. This central carbon is linked to:
 An amino group/ amine group
 Hydrogen
 A variable component known as the R-group/side chain
 A carboxylic group

One amino acid bond to another amino acid by the formation of a PEPTIDE BOND.

Long chains of bonded amino acids result in the formation of a protein.

Question 6

What is an oligopeptide?

Answer 6

*This is a peptide whose molecules contain a relatively small number of amino acids.
*Oligopeptides contain 2-20 amino acids

Question 7

How is an oligopeptide different from a polypeptide?

Answer 7

: The key difference between oligopeptide and polypeptide is that oligopeptides contain few amino acid residues, whereas polypeptides contain a large number of amino acid residues.

Question 8

Generally, how many amino acids that form proteins in living organisms?

Answer 8

There are twenty-two amino acids as the building blocks of proteins.

Question 9

Does every amino acid have a central carbon?

To which organic group is that central carbon bound?

Answer 9

1.Yes, every amino acid has a central carbon. This carbon is bond to:
 a carboxyl
 amino group
 an R-group
 Hydrogen

Question 10

What is the structural representation of carboxyl group?

Answer 10

The carboxyl (COOH) group is composed of a carbonyl group (C=O) and a hydroxyl group (O-H)

Question 11

What is the importance of the -R group (variable radical) in amino acid molecule?

Answer 11

The R-group is called a variable radical because it changes. It is an organic group that differs from one amino acid to the next.

It defines the amino acid’s properties (such as size and structure), helps predict its reactivity, charges, as well as the nature (polarity) of the amino acid i.e, if the amino acid is considered to be:
 Polar
 Nonpolar
 Basic
 Acidic
 Neutra

Question 12

Describe bond formation between two amino acids

Answer 12

The bond found in between polymers of proteins is called a peptide bond.

It is also a covalent bond that links amino acids together to form a polypeptide.

Through the process of dehydration synthesis or condensation reaction water molecules are liberated to link monomers of amino acids to form a polymer.

Amino acids consist of an amino group (NH2) and a carboxyl group (COOH) functional group.

During de-hydrolysis reaction the hydroxyl within the carboxyl group of amino acid 1 and the hydrogen within the amino group from amino acid 2, join together to form water and a dipeptide as products as shown in Fig a.

This reaction can repeat to form a linear polymer of 100 amino acids and more.

Question 13

Can the same total number of amino acids make different proteins?

Answer 13

The same total number of amino acids can make up different proteins, as varying of the sequencing of said amino acids will result in changes in the subsequent stages of protein formation (e.g., change in the folding pattern in the secondary stage) which results in formation of a protein with a different function and structure than that of one with a different sequence.

Question 14

Are proteins with the same number of each different amino acid that form them necessarily be identical proteins?

Answer 14

No, unless their amino acid sequence is identical.

Question 15

What is the essential condition for a protein to be identical to another protein?

Answer 15

They have to have identical sequence of amino acids..

Question 16

Describe the primary structure of a protein?

Answer 16

This is the unique linear sequence of amino acids in a protein linked together through peptide bonds formed during protein biosynthesis process to form a polypeptide chain.

*During protein synthesis, the carboxyl group of the amino acid at the end of the growing polypeptide chain reacts with the amino group of the incoming amino acid, releasing a molecule of water. The resulting bond between the amino acids is a peptide bond.

*The sequence is determined by the sequence of nucleotide bases in the gene encoding the protein.

*Other covalent bonds are included in the primary structure, and these are primarily the disulfide bonds between cysteine residues that are adjacent in space but not in the linear amino acid sequence

Question 17

What is the significance of the primary protein structure?

Answer 17

*It is responsible for the unique 3-dimensional shape of the protein during folding.

*Knowledge of the primary structures of normal and mutated proteins may be used to diagnose or study many genetic diseases that result in proteins with abnormal amino acid sequences, which cause improper folding and loss or impairment of normal function.

Question 18

How is the secondary protein structure generated?

Answer 18

The secondary structure describes the localized folded shape of a protein due to interactions of the peptide backbone and is stabilized by intramolecular and sometimes intermolecular hydrogen bonding of the amide groups.

*These hydrogen bonds form between the partially negative oxygen atoms and the partially positive hydrogen atoms

*The formation of these hydrogen bonds results in repeated folding of the amino acid, which gives rise to one of two localized conformations; alpha helix (α-helix) and the beta-pleated sheet (β-pleated).

Question 19

Describe the alpha -helix.

Answer 19

• In the rod-like α-helix, amino acids arrange themselves in a regular helical conformation. The carbonyl oxygen of each peptide bond forms a hydrogen bond with the hydrogen on the amino group of the fourth amino acid away.
• The hydrogen bonds run nearly parallel to the axis of the helix.
• There are 3.6 amino acids per turn of the helix, covering 0.5 nm.
• Each amino acid residue represents an advance of 0.15 nm along the axis of the helix
• The side chains are all positioned along the outside of the cylindrical helix

Question 20

Describe the β-pleated sheet.

Answer 20

β-pleated sheet
* Hydrogen bonds form between peptide bonds either in different polypeptide chains or in different sections of the same chain.
* The sidechains protrude above and below the sheet.
* Adjacent polypeptide chains can be either parallel or antiparallel depending on whether they run in the same direction or in opposite directions, respectively.
* The chains are fully extended with 0.35 nm distance from one carbon to the next

Question 21

Delineate the difference(s) between the alpha-helix and the beta-sheet protein conformations.

Answer 21

α-helix
*Has a spiral or curled ribbon shape
*Stabilized by intramolecular hydrogen bonds
*Can exist as a single chain
*Forms a rod-like structure
*The sidechains are positioned on the outside of the cylindrical helix

β-pleated
*Has a folded shape
*Stabilized b intermolecular hydrogen bonds
*Cannot exist as a single chain
*Forms a sheet-like structure
*The sidechains protrude above and below the sheet

Question 22

Describe the tertiary protein structure. What are the main types of tertiary structure?

What is a domain?

Answer 22

It refers to the entire three-dimensional conformation of a polypeptide chain of a protein which determines its function.

• Refers both to the folding of domains and the final arrangement of domains in the polypeptide.
• The polypeptide chain folds spontaneously so that the majority of its hydrophobic sidechains are buried in the interior while the majority of its polar, charged sidechains are on the surface.
• The 3-D conformation is maintained by hydrophobic interactions, electrostatic forces, hydrogen bonding, and covalent disulfide bonds if present.
• The electrostatic forces include salt bridges between oppositely charges groups and the multiple weak van der Waals interactions between the tightly packed aliphatic sidechains in the interior of the protein.

** A domain is a section of a protein sufficient to perform a particular chemical or physical task such as binding of a substrate or other ligand.

Question 23

There are 2 types of tertiary structures of proteins.

State the two types and name an example under each.
Differentiate between the 2 of them.

Answer 23

1.The main types of tertiary structure are the globular type and fibrous type.

2.Myoglobin and Collagen respectively.

3. FIBROUS PROTEIN

*Long and narrow
Polypeptide chains lie parallel to each other to form a fiber.

*Function: Structural protein.

*Stability: More stable.
Less sensitive to pH and temperature.

*Solubility: Generally, less soluble

*Relationship with water: Hydrophobic

GLOBULAR PROTEIN
*Round and spherical.
Polypeptide chains intertwine with each other to form a spherical

*Functional protein

• Less stable and denature easily.
  Sensitive to pH and temperature

*Generally, more soluble.

*Hydrophilic

Question 24

Explain what quaternary protein structure is.
a. Do all proteins have a quaternary structure?

Answer 24

1.*Refers to the spatial arrangement of polypeptide subunits and the nature of the interactions between them.

*The subunits are held by noncovalent interactions such as hydrogen bonding, electrostatic forces and hydrophobic interactions, and covalent links such as disulfide bonds.

2.Not all proteins have a quaternary structure because many proteins consist of a single polypeptide chain and are defined as monomeric proteins.

Question 25

Give details of bond(s) associated with folded protein structure.

Answer 25

Bonds associated with folded protein structure.

1. Hydrogen bonds
   *When two atoms bearing partial negative charges share a partially positively charged hydrogen, the atoms are engaged in a hydrogen bond (H-bond).

*The correct 3-D structure of a protein is often dependent on an intricate network of hydrogen bonds.

*These can occur between
 atoms on two different amino acid sidechains
atoms on amino acid sidechains and protein backbone atoms
atoms on amino acid sidechains and water molecules at the protein surface
backbone atoms on two different amino acids
backbone atoms and water molecules at the protein surface.

2. Covalent bonds - Disulfide bridges
   *A covalent bond arises when two atoms share a pair of electrons.
   *These are the strongest chemical bonds contributing to protein structure.
   *Covalent bonds between cysteine side chains can be important determinants of protein structure.
   *A disulfide bond is a covalent bond formed from the oxidation of the sulfhydryl group (-SH) of each of two cysteine residues to produce a cystine residue
   *The folding of the polypeptide chain(s) brings cysteine residues into proximity and permits covalent bonding of their side chains
   *Disulfide bonds contribute to the stability of the 3-D shape of a protein molecule and prevents it from being denatured in the extracellular environment..

Examples: insulin (has 2 disulfide bonds), oxytocin (hormone involved in smooth muscle contraction), immunoglobulins.

3.Ionic bonds
*When two oppositely charged groups are brought together, electrostatic force leads to strong interaction

*Intramolecular ionic bonds are infrequently used in the stabilization of protein structure.

*They are weaker than hydrogen bonds

*Responsible for maintenance of folded structure of globular proteins

4. Non-polar/ Hydrophobic bonds
   *Amino acids with non-polar sidechains tend to be in the interior of the polypeptide molecule, where they associate with other hydrophobic amino acids.
   * Amino acids with polar or charged side-chains tend to be located on the surface of the molecule in contact with the polar solvent.

Question 26

What is protein denaturation?

Answer 26

It is the process of unfolding the shape and structure of secondary, tertiary and quaternary levels of proteins.

Or

Loss of secondary, tertiary, and quaternary structures of protein resulting in loss in their functioning.

Question 27

Is there any change in the primary protein structure when a protein is denatured?

Answer 27

There is no change in the primary structure of proteins due to strong covalent peptide bonds.

Question 28

What is renaturation?

Answer 28

The protein denaturation can be reversible.
The process is known as renaturation.

*It is possible to convert denatured protein to its native protein structure under influence of a controlled
condition.

*For example, addition of salicylate on hemoglobin.

However, in extreme situations some proteins are unable to go back to their original state after denaturation.

Question 29

List factors that can lead to protein denaturation.

Answer 29

*pH
* temperature
* ultrasound
* UV light and radiation
* High pressure

Question 30

Is there a functional consequence of changes in Primary/Secondary/Tertiary Structures?

a. What are the effects of the changes?

b. Give examples of instances/diseases where all the structural levels of the protein is affected and how these changes occurred.

What is the impact of these changes in the particular example.

Answer 30

• Increased viscosity
• Increased ionizable groups. For example, sulfhydryl groups, disulphide groups
• Easy digestion of denatured proteins
• No change in primary structures

2.
* Parkinson’s disorder
* Alzheimer’s disease
* Sickle cell anemia
* Cystic fibrosis
* Huntington’s disease

3.
Cystic fibrosis- mutation of the CFTR gene leading to the misfolding of the CFTR protein. Thus, resulting in the production of the sticky thick mucus by cells that is
unable to be swept away by the cilia in trachea hence trapped bacteria by mucus stays in the lungs.

*Alzheimer’s disease- accumulation of the misfolded amyloid-β protein to form amyloid plaque in the brain that collect between neurons and disrupt cell function hence
result in neurotransmitters between brain cells.

*Sickle cell anemia- change in primary structure of beta globin chain in hemoglobin. The hydrophilic amino acid glutamic acid is replaced by the hydrophobic amino acid valine. When the red blood cell come in contact with water, it causes the hemoglobin chain to bend inwards resulting in the sickle shaped cell.

Question 31

Describe what essential amino acids are.

List all the essential amino acids.

Answer 31

They play critical roles in the body including tissue repair, protein formation and nutrient absorption.

They cannot be synthesized by the body fast enough to meet the demand in the body and must therefore come from the diet.

• Tryptophan
• Histidine
• Isoleucine
• Valine
• Threonine
• Phenylanine
• Methionine
• Leucine
• Lysine

We can remember them using the mnemonic “PVT TIM HaLL”.

Question 32

What are Protein-Protein Interactions?

Answer 32

Protein-Protein Interactions are the intentional physical contacts that are established between
two or more proteins, as a result of biochemical events and/or electrostatic forces.

PPI’s play important roles in various biological processes, including cell-to-cell interactions, cell cycle progressions, signal transduction, metabolic pathways and immune protection.

Question 33

Give four examples of protein-protein interactions.

Answer 33

*Muscle contraction: filaments of actin and myosin proteins are involved. These proteins slide past one another to bring about muscle contraction.

*Cellular transport: refers to carrier proteins and channel proteins.They cooperate to allow
transportation of substances between and within cells in the human body

*Cell signaling: protein kinase-substrate interactions. The activity of the cell is regulated by extracellular signals. Specific kinase binds to beads, which then interact in cell lysates.

*For the last example: docking marker proteins such as v-SNAREs hook up with docking marker receptors called t-SNAREs, to allow the fusion of the secretory vesicle membranes with plasma membranes