Topic A: BIOMOLECULES

Question 1

What is the structure of monosaccharides?

Answer 1

General formula: (CH2O)N
Has a carbonyl group (C=O) and multiple hydroxyl groups. (C=O is part of the aldehyde or ketone group)
It makes it either and aldose or ketose.

Question 2

What is the structure of glucose?

Answer 2

Chemical formula of C6H12O6
In solution, glucose alternates between straight chains and ring structures freely. It exists mainly in ring structure, and only a small proportion exists in straight chain.
There are two possible ring structure of glucose. A-glucose and B-glucose. A-glucose has OH on the bottom part of the C1. B-glucose has OH on the top part of C1 glucose.

Question 3

What is a hydrolysis reaction?

Answer 3

The glycosidic bond is broken between 2 monosaccharides in a hydrolysis reaction with the addition of one molecule of water, to form the hydroxyl group on 2 different monosaccharides.

Question 4

How are polysaccharides designed for storage?

Answer 4

They are large and insoluble, exerting no osmotic effect on cells when stored in large amounts and do not interfere with chemical reactions of the cells.
They are large and unable to diffuse out of the cells.
They fold into compact shapes and thus large amounts can be stored within fixed volume.
They are easily hydrolysed into monosaccharides when required by the cells.

Question 5

How are polysaccharides designed for STRUCTURE?

Answer 5

Structural polysaccharides are unbranched polymers.
They form long straight chains which are ideal for formation of strong fibres.

Question 6

What is the structure of starch?

Answer 6

Starch is a polymer consisting of A-glucose moleqs.
Consists of a mixture of 2 types of polymers, amylose and amylopectin.

Question 7

What is the structure of amylose?

Answer 7

Amylose:
Consists of several thousand A-glucose.
Linked by A-1,4-glycosidic bonds
Unbranched chain polymer, coiling into a helical compact structure stabilised by H bonds.
Hydroxyl groups on C2 of each glucose residue projects into the middle of the helix, H bonds are formed between the -OH group of adjacent glucose residues.

Question 8

What is the structure of amylopectin?

Answer 8

Twice as many glucose residues as amylose.
Linked by A-1,4-glycosidic bonds and A-1,6-glycosidic bonds.
Branched chain polymer. Coils into a helical, compact structure stabilised by hydrogen bonds.
Hydroxyl groups on C2 of each glucose residue projects into the middle of the helix and hydrogen bonds are formed between -OH group of adjacent glucose residues.

Question 9

What is the structure of starch in relation to its function?

Answer 9

Main energy storage in plants.
Accumulates to form starch grains in the chloroplast of plant cells
Compact structure allows many glucose molecules to be stored in a small volume within the cell.
Can be easily converted back into glucose for use in respiration to produce ATP. When necessary, free sugars are released by hydrolysis of starch.

Question 10

What is the structure of glycogen?

Answer 10

Glycogen has a structure similar to amylopectin.
It consists of A-glucose residues
Linked by A-1,4-glycosidic bonds and A-1,6-glycosidic bonds.
More extensive branching as compared to amylopectin, resulting in a more compact structure.
Coils into a helical, compact structure stabilised by H bonds.

Question 11

What is the function of glycogen?

Answer 11

Main energy storage molecule in animals.
Accumulates to form gylcogen granules in liver and muscle cells.
Compact structure allows many glucose molecules to be stored in a small volume within the cell.
Easily hydrolysed into glucose when required by the cells.

Question 12

What is the structure of cellulose?

Answer 12

Consist of B-glucose residues.
Linked by B-1,4-glycosidic bonds
Adjacent glucose molecules are rotated 180. with respect to each other.
Unbranched chain polymer
Straight chain of B-glucose run parallel to each other with numerous H bonds.
The cellulose chains associate in group to form bundles called microfibril, later forms macrofibrils
Macrofibrils of successive layers are interwoven and are embedded in a gel-like matrix, has high tensile strength

Question 13

What is the function of cellulose?

Answer 13

Main component of cellulose cell wall of plants for structural support.
Large intermolecular spaces between macrofibrils cause the cell wall to be permeable, allowing free movement of molecules in and out.

Question 14

How are triglycerides formed?

Answer 14

Triglycerides are formed from 3 fatty acid moleqs with 1 glycerol molecules by condensation.
3 ester bonds are formed with the removal of 3 water molecules.
The resulting triglyceride is non-polar
Each hydroxyl group in glycerol reacts with a carboxyl group in a fatty acid molecule to form an ester bond/linkage
Ester bonds can be broken by hydrolysis

Question 15

What are the properties of triglycerides?

Answer 15

Triglycerides can be classified as fats or oils. Fats are solid at 20°C. Consists of long saturated fatty acid chains Presence of single bonds thus packed tightly and more compact. More hydrophobic interactions between the fatty acid chains, resulting in higher melting points.
Oils are liquid at 20°C. Consists of relatively short unsaturated fatty acid chains Presence of double bonds results in kinks in the fatty acid chain, thus packed less tightly and less compact. Less hydrophobic interactions between fatty acid chains, resulting in lower melting points.
Solubility: They are insoluble in water but soluble in organic solvents
Density: Triglycerides have lower density than water and thus floats on water.

Question 16

Why are lipids adapted for energy storage?

There are more, but the ones here are the most relavant

Answer 16

Triglycerides are a respiratory substrate, having long hydrocarbon chains that can be hydrolysed and oxidised during respiration to produce energy in the form of ATP. Lipids have a higher calorific value than other respiratory substrates, releasing a higher amount of metabolic energy per unit mass as are there are more C-H bonds to release more ATP upon hydrolysis.
Lipids (38.9KJ/g) yield double the amount of metabolic energy on Oxidation than carbohydrates (17.2kJ/g). Triglycerides release twice as much metabolic water (1.07g/g lipid) as compared to carbohydrates (0.56g/g lipid) when oxidised in respiration.
Lipids can be stored in large amounts without exerting any osmotic effect on cells. They are large molecules and non-polar due to the presence of hydrocarbon tails thus insoluble in water. Therefore, they are unable to diffuse out of cells. They are less dense than carbohydrates as they are more compact and are unhydrated. Main energy source for highly active animals due to the demands of locomotion. Main energy storage for seeds dispersed by wind, resulting in a light seed which can be caried over longer distances.

Question 17

What is the structure of phospholipids?

Answer 17

Phospholipids are lipids containing a phosphate group
Made up of 1 glycerol molecule, 2 fatty acid molecules and 1phosphate group formed when one of the three hydroxyl groups in glycerol reacts with phosphoric acid and the other two -OH groups react with fatty acids as in the formation of triglycerides
Formed by a condensation reaction resulting in the formation of two ester bonds and one phosphoester bond with the removal of 3 water molecules
Amphipathic molecule due to the hydrophilic phosphate head and wo hydrophobic hydrocarbon / fatty acid chains The phosphate head is hydrophilic as it is charged
Thus the head of the molecule is soluble in water but the tails are insoluble in water
When placed in water, forms micelles and membrane bound.

Question 18

What is the structure of an amino acid?

Answer 18

The central carbon atom, known as the a-carbon is bonded to 4 different groups of atoms:
hydrogen atom
basic amino group (-NH:) which accepts protons
acidic carboxyl group (-COOH) which donates protons
R group/ side chain which is unique to each amino acid
Amino acids are classified into uncharged and charged R groups. Uncharged amino acids can be non-polar (glycine) or polar (cysteine). Charged R groups can be basic or acidic.

Question 19

What are the properties of amino acids?

Answer 19

Insoluble in organic solvents but can dissolve in water to form zwitterions.
Properties of amino acids
Dipolar as they carry a positive charge on the basic group and a negative charge on the acidic group.
Amphoteric, as they contain both acidic and basic groups. They are able to resist slight changes in pH, thus are able to act as pH buffers

Question 20

What is the peptide bond and how are they broken?

Answer 20

A peptide bond is the covalent bond between two amino acids. Peptide bonds are formed between the carboxyl group of one amino acid and the amino group of another in a condensation reaction with the removal of one molecule of water.
Peptde bonds can be broken by hydrolysis reactions using enzymes or acid hydrolysis The peptide bond is broken between two amino acids (in a dipeptide) in a hydrolysis reaction with the addition of one molecule of water, to form the amino group and the carboxyl group on two different amino acids.

Question 21

What are the 4 levels of structural organisation in proteins?

Answer 21

There are 4 levels of structural organisation in proteins: primary, secondary, tertiary and quaternary.

Question 22

Describe the primary level of protein organisation.

Answer 22

The primary structure is the specific number and sequence of amino acids joined by peptide bonds in a polypeptide chain.
Every protein molecule has a unique sequence of amino acids which is determined by base sequence of DNA. The unique sequence of amino acids with its side chains of different chemical and physical properties determines the three-dimensional conformation of the protein.
Every polypeptide possesses a carboxyl terminus (C-terminus) and amino terminus (N-terminus). The possible amino acid residues in a polypeptide chain can be of any number and arrangements of the 20 common amino acids.

(The total possible number of different combinations of polypeptide chains can be denoted as n’, wheren = number of different amino acids and r = number of residues in polypeptide chain.)

Question 23

Describe the secondary structure.

Answer 23

Secondary structure refers to the local spatial conformation of a polypeptide backbone, excluding the side chains of its amino acids. The secondary structure is the repeated coiling and folding of a polypeptide chain, maintained by hydrogen bonds fomed between peptide bonds
Hydrogen bonds are formed between N-H group in a peptide bond of an amino acid and C=O group in a peptide bond of another amino acid.
There are two main forms of secondary structures, namely a-helix and B-pleated sheets.

A-helix and B-pleated will be gone through in other cards.

Question 24

Describe the structure of an A-helix.

Answer 24

Unbranched polypeptide chain tightly coiled into a spiral Each turn of the helix consists of 3.6 amino acids Held by intra-chain hydrogen bonding between N-H group in a peptide bond of an amino acid and C=O group in a peptide bond of another amino acid four amino acids away.
The numerous hydrogen bonds make the a-helix structurally strong and inelastic but flexible.

Question 25

Describe the structure of the B-pleated sheets.

Answer 25

Consist of extended adjacent regions of a Single polypeptide chain arranged in a parallel or antiparallel manner.
Held together by hydrogen bonding which exists between the N-H group in a peptide bond of a region of the chain and C=O group in a peptide bond of an adjacent region of the same chain.
Pleated appearance of the B-pleated sheet arises from the tetrahedral chemical bonding at the A-carbon atom
The numerous hydrogen bonds make the structure very stable and rigid. The sheet also has high tensile strength thus it cannot be stretched.

Question 26

Describe the tertiary structure?

Answer 26

Tertiary structure is the compact unique three-dimensional conformation due to further coiling and folding of secondary structures. The tertiary structure of a protein is held by hydrogen bonds, ionic bonds, disulfide bonds, and/or hydrophobic interactions between R groups/side chains of amino acids on a single polypeptide chain.

Question 27

Describe the bonds that allow for a tertiary structure protein to be formed.

H2ID

Answer 27

1. Hydrogen bonds
   Hydrogen bonds are formed between an electronegative atom and a hydrogen atom bonded to another electronegative atom (such as nitrogen or oxygen) Each hydrogen bond is weak. However, a large number of weak hydrogen bonds are sufficiently strong to hold protein structure together.
2. Ionic Bonds
   Electrostatic atraction between positively and negatively charged R groups. Relatively strong, although easily disrupted by changes in pH.
3. Disulfide bonds
   Strong covalent bond (S-S) Formed from oxidation of sulphydryl (-SH) groups of two neighbouring cysteine R groups. Only cysteine contains a sulphydryl (-SH) group in its R group. Very strong and not easily broken except by reducing agents.
4. Hydrophobic interactions
   Weak interactions between non-polar R groups. When a polypeptide chain with non-polar amino acids is placed in an aqueous medium, the chain will fold such that the non-polar R groups are in close contact and shielded from the aqueous medium.

Question 28

Describe the quartenary structure.

Answer 28

Quatemary structure is when more than one polypeptide chain is held together by hydrogen bonds, ionic bonds, disulfide bonds and/or hydrophobic interaction between R-groups of different polypeptide chains. E.g. haemoglobin is a protein comprises four polypeptide chains.
Quatemary structure involves inter-chain interactions, in addition to the intra-chain interactions seen in the primary, secondary and tertiary structure.

Question 29

What is the structure of haemoglobin?

Answer 29

Haemoglobin is a quartenary globular protein, consisting of 2 identical A-chains of 141 AA, 2 B-chains of 146AA. Each polypeptide is coiled into A-helices and then folded into a spherical globular shape.
Hydrophobic amino acid residues are in the interior of the folded structure, and hydrophilic amino acid residues are found at the exterior surface to maintain solubility of the protein.
The 4 polypeptides are held by hydrophic interactions, ionic bond, and hydrogen bond.
Haem groups
A porphyrin ring with Fe2+ in the centre, binding to an oxygen molecule reversibly.
Each haem group resides in a hydrophobic pocket in the teriatry structure of a polypeptide chain. Hence, a haemoglobin moleq has 4 haem groups and can carry 4 O2 molecules to form oxyhaemoglobin.

Question 30

What is the structure in relation to function of haemoglobin?

Answer 30

1. The hydrophobic amino acids in the interior of the protein and hydrophilic amino acids found at the exterior surface of the protein. Allow the haemoglobin to be soluble to take part in chemical reactions.
2. The haem group, a porphyrin ring with an iron ion (Fe2+) centre, is held in the hydrophobic pocket of the polypeptide chain, Allow haemoglobin to þind reversibly to oxygen and transport oxygen to the rest of the body
3. The quaternary structure, of four subunits, are held by weak bonds such as hydrophobic interactions, ionic bonds and hydrogen bonds Allows cooperative binding of oxvgen to haemoglobin Binding of one O2 molecule to one subunit results in a conformation change of the adjacent subunits in the haemoglobin molecule, making it easier for another O2 molecule to bind with the other haem groups in the molecule. This increases the rate of uptake of oxygen by haemoglobin.
4. Haemoglobin is a globular protein and is folded into a spherical shape. Allow the protein to be compact and many haemoglobin molecules to be dissolved in the cytoplasm of a red blood cell.

Question 31

What is the structure of collagen?

Answer 31

Fibrous protein performing a structural and supportive function in skin, bone Connective tissue and tendons.
Basic structural unit of collagen is tropocollagen, which comprises 3 polypeptide chains wound around each other to form a triple helix. 1050 amino acids residues in each chain. Has a high proportion of glycine, proline and hydroxyproline
A repeated triplet sequence of Gly-X-Y o 1/3 of amino acid residues are glycine. Xis often proline, and Y is often hydroxyproline.
Proline and hydroxyproline are bulky and relatively inflexible Each of the three polypeptide chains is coiled into a helix (not to be confused with a-helix).

Question 32

What is the structure of collagen in relation to its function?

Answer 32

1. Every 3rd amino acid residue is a glycine and this allows each helical chain to makes a tun every 3 residues and intertwine around two other chains to form the triple helix, as only glycine is small enough to fit into the centre
   Allows the structure to be very compact
2. The 3 helical chains are held together by hydrogen bonds forming tropocollagen Allows the structure to be relatively rigid.
3. Hydrophobic amino acids are found at the exterior surface of collagen. Allows it to be insoluble in water (distinct feature of fibrous proteins) and metabolically inactive, and thus, resistant to chemical changes.
4. Many triple helices lie parallel in a staggered pattern to form fibrils, with covalent bonds between neighbouring triple helix chains. Fibrils unite to form fibres. Allows collagen to have high tensile strength, and high resistance to stretching

Question 33

What is the G-protein linked receptor?

Answer 33

Transmembrane protein embedded in the cell surface membrane of a specific cell responsible for cell signalling. For a cell to respond when it encounters a signal, the signal must first be recognised by a specific receptor molecule on the cell surface and then transmitted to the cell’s interior before an appropriate cellular response can occur

Question 34

What is the structure of G protein?

Answer 34

Each GPLR is closely associated with a G protein, a protein that binds to guanosine triphosphate (GTP) or guanosine diphosphate (GDP) The heterotrimeric G protein consists of three different subunits and Gy. Ga, GB Ligand The Ga subunit binds either GDP or GTP. GTP is an energy molecule similar to ATP.

Question 35

What is the structure of G protein in relation to function?

Answer 35

S: Single polypeptide chain with seven hydrophobic transmembrane a-helices
F: Allows the protein to be embedded within the cell membrane by forming hydrophobic interactions with the fatty acid chains
S: Extracellular amino terminus and specific loops between the helices
F: Allows the protein to have an extracellular ligand binding site Intracellular carboxyl terminus and specific loops between the helices .Allows the protein to have an intracellular G protein binding site

Question 36

Why does denaturation work?

Answer 36

A protein’s specific 3-dimensional conformation determines its biological function which may involve recognising and binding to other molecules. Denaturation is the loss of the specific 3-dimensional confomation of a protein molecule. This involves the breakage of bonds maintaining protein structure, resulting in the protein losing its biological function. Depending on the degree of denaturation, the molecule may partially or completely lose its biological activity.
The change may be temporary or permanent.

Question 37

What factors cause denaturation?

Answer 37

1. Temperature
   High temperature increases kinetic energy and causes atoms in proteins to vibrate disrupting weak.hydrophobic interactions, hydrogen bonds and ionic bonds
2. pH
   A drastic change in pH affects charged and polar R-groups and disrupts ionic bonds and hydrogen bonds of proteins. If the medium is too acidic (sudden increase of H’ ions), the acidic R-group CO0 will accept H’ ions to form COOH. If the medium is too basic (sudden decrease of H’ ions), the basic R-group NHs will donate H ions to form NH2. If either COOH or NH2 are no longer charged, ionic bonds will be disrupted Presence of very high concentration of H may even cause peptide bonds to be broken (acid hydrolysis).
3. Heavy Metals
   Heavy metal ions are positively charged and form strong bonds with negatively-charged carboxyl R-groups of proteins, disrupting ionic bonds Exampiles of heavy metal ions are Fe, Cu, Pb, Ag, Zn. GroupI and Il metal ions are not heavy metal ions. With less negative charges on the protein, the solubility of protein is reduced as there is less interaction with polar water molecules.
4. Redox agents
   Reducing/ oxidising agents disrupt disulfide bonds formed between cysteine thus causing proteins to lose their 3-dimensional conformation
5. Organic solvents
   Organic solvents and detergents disrupt hydrogen bonding and hydrophobic interactions of proteins, respectively.