Proteins

Question 1

Describe how a functional protein comprise of amino acids:

Answer 1

Amino acids are covalently joined by peptide bonds to form a polypeptide. They are subsequently folded into higher order structures, before assuming its specific 3D conformation

Question 2

Name the differences in the classification of proteins based on shape:

Answer 2

Fibrous proteins (Collagen, myosin, fibroin in silk, actin, keratin elastin) 
vs 
Globular proteins (Enzymes, hormones, antibodies, and haemoglobin)

Polypeptide chains are elongated and wound around each other to form rope-like structures
vs
Polypeptide chains are folded, bent and twisted to form a compact and spheroidal structure

Each chain has a repetitive amino acid sequence
vs
Each chain has a specific, non-repetitive amino acid sequence

Each chain is limited to a small, specific variety of amino acids
vs
Each chain is made up of a wide variety of amino acids

Amino acid sequence may vary slightly between two samples of the same fibrous protein
vs
Amino acid sequence never varies between two samples of the same globular protein

The length of the polypeptide chain may vary in two samples of the same fibrous protein
vs
The length of the polypeptide chain is always identical in two samples of the same globular protein

Fibrous proteins have stable structures due to the numerous intra- and inter-molecular hydrogen and covalent bonds
vs
Globular protein have relatively unstable structures due to numerous intra- and inter-molecular non-covalent bonds , such as hydrogen, ionic and hydrophobic interaction.

Fibrous proteins are generally insoluble in water
vs
Globular proteins are generally more soluble in water than fibrous protein

Fibrous proteins perform structural functions
vs
Globular protein perform metabolic functions

Question 3

Name the different types of proteins and their various functions:

Answer 3

Enzymatic proteins - Selective acceleration of chemical reactions (Digestive enzymes catalyse the hydrolysis of food)

Defensive proteins - Protection against disease (Antibodies inactivate and help destroy virus and bacteria)

Storage proteins - Storage of amino acids (Casein, protein in milk, is a major source of amino acids for baby mammals, Plants have storage proteins in their seeds. Ovalbumin is the protein in egg whites and is a source of amino acids for the developing embryo)

Transport proteins - Transport substances (Haemoglobin transport oxygen from the lungs to other parts of the body. Carrier proteins and channel proteins transport molecules across membranes)

Hormonal proteins - Coordination of an organism’s activities (Insulin)

Receptor proteins - Response of cell to chemical stimuli (Receptors built into the membrane of a nerve cell detect neurotransmitter molecules (signaling) release by other nerve cells)

Contractile and motor proteins - Movement (They are responsible for the undulations of cilia and flagella. Actin and myosin are responsible for the contraction of muscles)

Structural proteins - Support (Keratin, collagen, elastin, silk fibers)

Question 4

Name the difference in proteins classified based on composition:

Answer 4

Simple proteins: Only amino acids form the structure of simple proteins (Albumin, Globulin, Histones)

Conjugated proteins: The protein is combined with a cofactor (a non-protein component)
A cofactor aids protein function, can be inorganic or organic nature. A prosthetic group is known when an organic cofactor is tightly bound to a protein.
(Glycoprotein: Carbohydrate - blood plasma, cell membrane)
(Chromoprotein: Pigment - haemoglobin has haem an iron containing pigment, phytochrome is plant pigment)
(Lipoprotein: Lipid - membrane structur)
(Flavoprotein: FAD (flavin adenine dinucleotide) - Impt in electron transport chain in respiration)
(Nuceloprotein: Nucleic acid - component of viruses, chromosomes, ribosome structure)

Question 5

Name ways to classify proteins:

Answer 5

• Shape
• Function
• Composition

Question 6

Structure of an amino acid:

Answer 6

• Basic amine group (-NH2)
• Acidic carboxyl group (-COOH)
• Hydrogen atom
• Variable group/R group (aka side chain)

Question 7

Properties of amino acids:

Answer 7

Ability to form zwitterions* - Amino acids are insoluble in organic solvents but soluble in water where they form ions. This is because the amine and carboxyl group of amino acids can readily ionise.
*Zwitterion is an ion containing one positive and one negative charge, and is therefore electrically neutral, dipolar

Ability to act as a buffer - Since they exist as zwitterions in aqueous medium, amino acids are amphoteric, i.e. they have both acidic and basic properties in aqueous solution. As such, they can act as buffers in solutions (Buffer - a substance that can resist change in pH in a solution when a small amt of acid/akali is added)

Unique R group - R groups have important physical (size & shape) and chemical properties that influence the physical and chemical properties of free amino acids and proteins

Question 8

How do you classify amino acids based on their chemical properties?

Answer 8

• Non-polar amino acids (Hydrophobic)
• Polar amino acids (Hydrophilic)
• Charged amino acids (Hydrophilic)

Non-polar, neutral:
R-groups of these amino acids are hydrocarbon in nature, i.e. R-group has many C-H and C-C bonds.
Amino acids in this category are hydrophobic and unreactive. They tend to be localised in the interior ( i.e. they tend to be shielded from aqueous medium of the polypeptide as it folds into its 3D-conformation)

Polar, neutral:
These amino acids have polar R-groups (OH & -NH) with no net charge. These amino acids are hydrophilic in nature.

Charged, acidic & basic:
These amino acids have charged R-groups. They contain either a negatively charged or positively charged R group, making them hydrophilic.
Acidic amino acids have a net negative charge when ionised in water > carboxyl group in R- group
Basic amino acids have a net positive charge when ionised in water > amine group in R-group

Question 9

What is a peptide bond?

Answer 9

A peptide bond is a covalent bond joining one amino acid to another. A C-N bond is formed between the amine group (-NH2) of one amino acid and the carboxyl group (-COOH) of the other.

This process is a condensation reaction and eliminates a water molecule (release). The compound formed is a dipeptide.

Question 10

Briefly describe the levels of organisation in proteins

Answer 10

Linear sequence > Shape of amino region > Fold into 3 dimensional shape > Multiple polypeptides

Primary structure - Linear sequence of amino acids (peptide bonds)

Secondary structure - Certain sequences of amino acids form hydrogen bonds that cause the region to fold into a spiral (alpha helix) or pleated sheet (beta sheet)

Tertiary structure - Secondary structures and a random coiled region fold into a 3 dimensional shape

Quaternary structure - Two or more polypeptide may bind to each other to form a functional protein

Question 11

How is an amino acid sequence in a polypeptide chain synthesised?

Answer 11

Proteins are synthesised in vivo by the stepwise polymerisation of amino acids in the order specified by the sequence of nucleotides in a gene

Question 12

What determines the protein’s structure and function

Answer 12

The three higher levels of protein organisation -secondary, tertiary, and quaternary structures - are direct consequences of the primary structure.

The sequence of the amino acids in the protein rather than amino acid composition will influence the characteristics of a protein

The amino acid R-groups determine the type and location of bonds present at higher levels of organisation in the protein

Question 13

What factors of R-groups in amino acids affects the ultimate 3D conformation of the protein? (SPCH)

Answer 13

Size
Charge
Polarity
Hydrophobicity

Question 14

Describe the shape of the alpha-helix

Answer 14

It has the form of an extended spiral spring

Question 15

Describe the shape of the beta-pleated sheet

Answer 15

It takes on an extended zigzag, sheet-like conformation

Question 16

Special characteristic of beta-pleated sheets

Answer 16

Hydrogen bond can occur along two or more segments of the same polypeptide chain (Intrachain sheet) or different polypeptide chains (Interchain sheets)

They also come in two varieties:
Antiparallel beta-pleated sheet - neighbouring hydrogen-bonded polypeptide segments run in opposite N-terminus to C-terminus directions
Parallel beta-pleated sheet - hydrogen-bonded segments run in the same N-terminus to C-terminus direction.

Amino acids with bulky R-groups interfere with formation of the beta-pleated sheet by causing steric hindrance. As such, amino acid residue in a beta-pleated sheet usually have small R-groups

*Insert pictures ig

Question 17

Briefly define the tertiary structure in a functional protein

Answer 17

Tertiary structure refers to the further bending, twisting, and folding of the polypeptide chain with the secondary structures to give an overall specific 3D conformation of a protein.

Question 18

Name the bonds that determines the specific 3D conformation

Answer 18

The specific 3D conformation is determined by four types of R group interactions that are formed between amino acid residues some distance apart on the same chain:
Non-covalent interactions (relatively weak)
- Ionic bonds
- Hydrogen bonds
- Hydrophobic interactions
Covalent bonds (strong
- Disulfide bonds

Question 19

Describe the disulfide bonds present during R-group interaction that maintain specific 3D conformation

Answer 19

A disulfide bond/linkage is a covalent bond (strong) that is formed by oxidation of the sulfhydryl groups (-SH) of any two cysteine residue (intrachain & interchain)

Breakage via reduction

Question 20

Why are nails stronger than hair even though they are both made form keratin?

Answer 20

Nails have more disulfide bonds than hair. Thus it is stronger. They are both made of the same protein, folded into the same structure though.

Question 21

Describe the hydrogen bonds present during R-group interaction that maintain specific 3D conformation

Answer 21

A hydrogen bonds is formed between an electropositive hydrogen atom such as that attached to nitrogen or oxygen (H in -NH or -OH groups), and another electronegative atom (N or O atom) within the polypeptide chain

While each hydrogen bond is weak, the large number of hydrogen bonds confer stability to the protein.

Question 22

Describe the ionic bonds present during R-group interaction that maintain specific 3D conformation

Answer 22

Some amino acid R groups are positively charged (NH3+ group) while others are 
negatively charged (COO- group). These oppositely charged R groups may form 
ionic bonds.

These ionic bonds are relatively weak in the aqueous cellular environment and may be
broken by changes in the pH of the surrounding medium.

Question 23

Describe the hydrophobic interaction present during R-group interaction that maintain specific 3D conformation

Answer 23

The polypeptide folds so as to shield hydrophobic R-groups from the aqueous environment.

Interactions occur between hydrophobic R-groups of amino acid residues.

Question 24

Define the quaternary structure in a functional protein

Answer 24

Quaternary structure is the overall protein structure that results from the association of two or more polypeptide chains to form a functional protein.

e.g. Haemoglobin and collagen

Proteins with more than one polypeptide or subunit is known as multimeric proteins

Question 25

Describe the nature of these bonds in the quaternary structure

Answer 25

The same types of interactions that produce tertiary structure also contribute to quaternary structure - these include ionic bonds, hydrogen bonds, hydrophobic interactions and disulfide bonds between R groups of different protein subunits

Question 26

Briefly describe the molecular structure of haemoglobin and structure of individual subunits

Answer 26

The haemoglobin molecule is a multimeric protein comprising 4 polypeptide chains, namely 2 a-chains and 2 b-chains. It is a tetramer, comprising of two dimers.

Secondary structure
Each polypeptide chain consists of eight a-helices (named by letters A to H, starting from the N-terminus) connected by non-helical segments. Hydrogen bonds stabilise the eight a-helices.

Question 27

Explain how the tertiary structure of haemoglobin relates to the function it plays

Answer 27

Structure: Each polypeptide chain is folded such that amino acid residues located at the surface of a subunit are generally hydrophilic while those buried in the interior of the molecule are mostly hydrophobic.
Function: This makes haemoglobin soluble in an aqueous medium and hence, a good transport protein for oxygen in blood.

Structure: Folding of the polypeptide chain also allows the formation of a hydrophobic cleft (lined with hydrophobic amino acid residues) to allow for the haem prosthetic group to bind. Each polypeptide chain also contains a haem prosthetic group.
Function: Each haem group will bind 1 molecule
of O2. Therefore, each haemoglobin molecule will bind to 4 molecules of O2.

Structure: Each ahem group consists of a iron ion (Fe2+) held in a polyphyrin ring
Function: The iron ion, Fe2+, binds one of the oxygen atoms in a molecule of O2. The Fe2+ can combine reversibly with O2 and enhances the release of O2 in metabolically active tissues such as muscles.

Question 28

Briefly explain the quaternary structure of haemoglobin molecule

Answer 28

The two subunits in each dimer are held together primarily by hydrophobic interactions. However, ionic and hydrogen bonds also occur. The four subunits form a globular molecule that is held by multiple non-covalent interactions

Question 29

Explain how the quaternary structure of haemoglobin relates to the function it plays

Answer 29

As Fe2+ in the first haemoglobin subunit bind 1 molecule of O2, the F-helix(?) is pulled closer to the haem group.
This pull creates a strain on the haemoglobin subunits, such that the previously obscured haem groups of the other subunits are revealed.
Hence the remaining subunits changed their 3D conformation slightly, allowing their respective haem groups to bind to O2 more readily. (The remaining subunits’ affinities for O2 molecules increases.
Therefore, haemoglobin is known as an allosteric* protein, and this mechanism of oxygen binding is known as cooperativity/cooperative binding.

• An allosteric protein is one in which the binding of a ligand, e.g. O2 in the case of haemoglobin, to one site affects the binding properties of another site on the same protein.

Question 30

Explain the importance of subunit cooperativity in haemoglobin and relate it to the haemoglobin’s oxygen dissociation curve

Answer 30

Haemoglobin is made up of four polypeptides, which displays subunit cooperativity. Thus the oxygen-dissociation curve of haemoglobin is sigmoidal. The significance of such a sigmoidal
curve is:
- Oxygen is loaded onto haemoglobin in the lungs where the partial pressure is high, and
unloaded from haemoglobin in the rest of the body tissues where the partial pressure is low,
and
- When O2 is high, more haemoglobin subunits are bound to O2 and the haemoglobin is more
saturated with O2. The reverse occurs when O2 is low.

Subunit cooperativity thus allows haemoglobin to be an efficient oxygen earner, since
haemoglobin loses oxygen guickly in an environment with low oxygen concentration (such as in the muscles) and vice versa (such as in the lungs).

Question 31

Explain the difference between the difference between the oxygen dissociation curve of myoglobin and haemoglobin and its consequences regarding binding to oxygen

Answer 31

Myoglobin is made up of only one polypeptide. Thus, oxygen-dissociation curve of myoglobin is
hyperbolic.
[From the curve,] Myoglobin has a higher affinity binding to oxygen (i.e. more saturated with oxygen) than haemoglobin at the same partial pressure.

Question 32

Describe the key physical characteristics of collagen

Answer 32

It has strong, insoluble fibres that have great tensile strength

Question 33

Describe the primary structure of collagen and relate to its function

Answer 33

The amino acid sequence of a collagen polypeptide consists of a repeating tripeptide sequence of glycine and two other amino acids (e.g proline, hydroxyproline or hydroxylysine)

Question 34

How do we know that collagen is a fibrous protein?

Answer 34

Each collagen polypeptide assumes a left-handed helical conformation with about three residues per turn known as the collagen helix resembles a stretched-out helix). This regular repeated structure is a hallmark of a secondary structure and is indicative of a fibrous protein.

Question 35

Describe the quaternary structure of collagen and relate it to its function

Answer 35

Three parallel a-chains wind around each other with a gentle, right-handed, rope-like twist (i.e. right-handed triple-helix) to form the basic structural unit of collagen known as a tropocollagen.

The well-packed, rigid triple-helix structure is responsible for its characteristic tensile strength. The twist in the helix cannot be pulled out under tension because its component polypeptide chains are supertwisted about each other.

Question 36

Describe the key features of tropocollagen and relate it to its function

Answer 36

Every third residue of each polypeptide passes through the centre of the triple-helix, which is so crowded that only the small R group of glycine (Giy) can fit in. This explains the absolute requirement for Gly at every third residue.
- This allows the three helical a-chains to pack tightly together, which provides high tensile strength

The tropocollagen is held together by an extensive network of hydrogen bonds. Hydrogen bonds formed between the N-H group of Gly residue in one a-chain and the C=O group of another amino acid residue in a neighbouring a-chain help hold the three chains together. The hydroxyl groups (-OH) of hydroxyproline and hydroxylysine residues also participate in interchain hydrogen bonding. In addition, covalent cross-links are also present within tropocollagen molecules to further impart the collagen fibre with high tensile strength.

Question 37

Describe how the interaction the quaternary structure of tropocollagen allows it to fulfill its function

Answer 37

The tropocollagen is held together by an extensive network of hydrogen bonds. Hydrogen bonds formed between the N-H group of Gly residue in one a-chain and the C=O group of another amino acid residue in a neighbouring a-chain help hold the three chains together. The hydroxyl groups (-OH) of hydroxyproline and hydroxylysine residues also participate in interchain hydrogen bonding. In addition, covalent cross-links are also present within tropocollagen molecules to further impart the collagen fibre with high tensile strength.

Question 38

How is a collagen fibre formed from tropocollagen?

Answer 38

Many of these tropocollagen molecules lie side by side, linked to each other by covalent cross-links between the carboxyl end of one molecule and the amino end of another. This gives rise to a structure known as a collagen fibril.
The increasingly rigid and brittle character of aging connective tissue results from accumulated covalent cross-links in collagen fibrils.
The tropocollagen molecules are arranged in a staggered manner with each other. This arrangement is stabilised by hydrophobic interactions between tropocollagen molecules. This confers collagen greater strength.
The aggregation of collagen fibrils thus form a collagen fibre.

Question 39

Why does ageing have an effect on bone and connective tissue strength? (osteoporosis)

Answer 39

The increasingly rigid and brittle character of aging connective tissue results from accumulated covalent cross-links in collagen fibrils.

Question 40

Briefly describe denaturation

Answer 40

Denaturation involves disruption of the secondary, tertiary and quaternary structures, i.e. disrupts basically everything except primary structures

It disrupts:

• R group interactions such as disulfide bonds, ionic bonds, hydrogen bonds and hydrophobic interactions; and
• Hydrogen bonds formed between the N-H and C=O groups of the polypeptide backbone.

Question 41

Describe the effects of denaturant on the protein

Question 42

Describe the effects of denaturant on the protein

Question 43

Name the different types of denaturants

Answer 43

Heat, changes in pH, organic solvents, and urea detergents

Question 44

Describe the effects of a denaturant on the protein

Answer 44

Heat - Excessive heat increases vibrations of the atoms, leading to disruption of hydrogen bonds, ionic bonds and hydrophobic interactions.
Application: egg white becomes opaque during heating because the denatured proteins are insoluble and solidify.

Changes in pH - Drastic changes in pH changes the charges in the acidic and basic R-groups, leading to disruption of ionic bonds and hydrogen bonds

Organic solvents - Transfer of a protein from an aqueous environment to an organic solvent can disrupt hydrophobic interactions that make up the stable core of globular proteins. The protein turns inside out and the hydrophobic regions changes place with the hydrophilic regions.

Urea - Addition of chemicals can disrupt ionic and hydrogen bonds that maintains the protein’s conformation.

Question 45

Name the types of bonds found in each level of structure

Answer 45

Primary - Peptide bonds (amide bonds between the α-carboxyl group of one amino acid and the α-amino group of another)

Secondary - hydrogen bonds (N-H group of one amino acid and C=O group of another amino acid along the polypeptide backbone)

Tertiary - Disulfide bonds, hydrogen bonds, hydrophobic interactions, ionic bonds

Quaternary - Same as tertiary