Biological Molecules (AS level Bio)

By: Dr.Mufaddal Page 1

Biological Molecules

From small to large

1. The larger biological molecules are made from smaller molecules. Polysaccharides are made from monosaccharaides, proteins from amino acids,

nucleic acids from nucleotides, lipids from fatty acids and glycerol.

2. Polysaccharides, proteins and nucleic acids are formed from repeating identical or similar subunits

called monomers, and are therefore polymers. These build up into large molecules called macromolecules.

3. The smaller units are joined together by condensation reactions.

Condensation involves removal of water. The reverse process, adding water, is called hydrolysis and is used to break the large molecules back down into smaller molecules.

4. The linkages that join monosaccharaides are called glycosidic bonds. The

linkages that join amino acids are called peptide bonds.

Carbohydrates

5. Carbohydrates have the general formula Cx(H2O)y and comprise monosaccharaides, disaccharides and polysaccharides.

6. Monosaccharaides (e.g. glucose) and disaccharides (e.g. sucrose) are very

water-soluble and together are known as sugars.

7. Monosaccharaides are the smallest carbohydrate units. Glucose is the most common. They are important energy sources in cells and also important building

blocks for larger molecules like polysaccharides.


8. Monosaccharaides may have straight-chain or ring structures and may exist in different isomeric forms such as -glucose and -glucose. 9. Benedicts reagent can be used to test for reducing and non-reducing sugars. The test is semi quantitative.

10. Polysaccharides include starch, glycogen and cellulose.

11. Starch is an energy storage compound in plants. It is made up of two types of molecule, amylose and amylopectin, both made from -glucose. Amylose is an un-branching molecule, whereas amylopectin has a branching structure. Iodine solution can be used to test for starch. 12. Glycogen is an energy storage compound in animals, which is also made

from -glucose. Its structure is similar to that of amylopectin, but with more branching.

13. Cellulose is a polymer of -glucose molecules. The molecules are grouped together by hydrogen bonding to form mechanically strong fi bres with high

tensile strength that are found in plant cell walls.

Lipids

14. Lipids are a diverse group of chemicals, the most common of which are triglycerides (fats and oils).

15. Triglycerides are made by condensation between three fatty acid molecules

and glycerol. They are hydrophobic and do not mix with water. They are energy storage compounds in animals, as well as having other functions such as

insulation and buoyancy in marine mammals.

16. Phospholipids have a hydrophilic phosphate head and two hydrophobic fatty acid tails. This is important in the formation of membranes.

17. The emulsion test can be used to test for lipids.

Proteins

18. Proteins are long chains of amino acids which fold into precise shapes. The sequence of amino acids in a protein, known as its primary structure,

determines the way that it folds and hence determines its three dimensional shape and function.

19. Many proteins contain areas where the amino acid chain is twisted into a

-helix; this is an example of secondary structure. The structure forms as a result of hydrogen bonding between the amino acids.


Another secondary structure formed by hydrogen bonding is the -pleated sheet.

20. Further folding of proteins produces the tertiary structure. Often, a protein

is made from more than one polypeptide chain. The association between the different chains is the quaternary structure of the protein. Tertiary and

quaternary structures are very precise and are held in place by hydrogen bonds, disulfide bonds (which are covalent), ionic bonds and hydrophobic interactions.

21. Proteins may be globular or fibrous. A molecule of a globular protein, for

example hemoglobin, is roughly spherical. Most globular proteins are soluble and metabolically active. Hemoglobin contains a non-protein (prosthetic) group,

the Haem group, which contains iron. This combines with oxygen. A molecule of a fibrous protein, for example collagen, is less folded and forms long strands.

Fibrous proteins are insoluble. They often have a structural role. Collagen has high tensile strength and is the most common animal protein, being found in a

wide range of tissues. 22. Biuret reagent can be used to test for proteins.

Water

23. Water is important within plants and animals, where it forms a large part of

the mass of each cell. It is also an environment in which organisms can live.

24. As a result of extensive hydrogen bonding, water has unusual properties that are important for life: it is liquid at most temperatures on the Earths surface; its highest density occurs above its freezing point, so that ice fl oats and insulates water below from freezing air temperatures; it acts as a solvent

for ions and polar molecules, and causes non-polar molecules to group together; it has a high surface tension, which affects the way it moves through

narrow tubes and forms a surface on which some organisms can live. Water can also act as a reagent inside cells, as in hydrolysis reactions and in photosynthesis as a source of hydrogen.


Multiple - choice Test

1 The results of testing a solution for the presence of three biological molecules are shown in the table.

Which biological molecules are present in the solution?

A reducing sugar and protein

B reducing sugar and starch C protein only

D starch only 2 The diagrams show the structure of four monosaccharaides.

Which row in the table below identifies -glucose and -glucose?


3 Which reaction involves the hydrolysis of glycosidic bonds?

A cellulose glucose B glucose glycogen C protein amino acids D triglyceride fatty acids and glycerol

4 The diagram shows a tripeptide made from three glycine amino acids.

Which of the bonds numbered 1 to 8 represent peptide bonds?

A 1 and 7

B 2 and 8 C 3 and 6

D 4 and 5

5 The following bonds are among those found in proteins: disulfide, hydrogen, ionic and peptide bonds.

Which row shows the bonds involved in primary, secondary and tertiary protein structures?


6 Which of the following describes a molecule of hemoglobin?

A a central haem group enclosed by four coiled globin polypeptides B a central globin group enclosed by four coiled haem polypeptides

C four coiled globin polypeptides, each with a central haem group D four coiled haem polypeptides, each with a central globin group

7 Which statement about the properties of water is not correct?

A Evaporation of water is an effective means of cooling an organism.

B Large volumes of water are slow to change temperature as the environmental temperature changes.

C The solid form of water, ice, is denser than the liquid form. D Water is an excellent solvent for ions and polar molecules.

8 Amylopectin is formed from amylose by a plant cell detaching short lengths of

an amylose chain and reattaching them as branches. Which bonds are broken and which are formed when amylose is converted into amylopectin?

9 The graph shows the variation in melting point of triglycerides with different numbers of carbon atoms in their fatty acid chains.


What explains these results?

A Triglycerides with longer fatty acid chains have stronger intermolecular forces and so have a lower melting point.

B Triglycerides with longer fatty acid chains have weaker intermolecular forces and so have a higher melting point.

C Triglycerides with shorter fatty acid chains have stronger intermolecular forces and so have a higher melting point.

D Triglycerides with shorter fatty acid chains have weaker intermolecular forces and so have a lower melting point.

10 In spider silk, the polypeptide chains have the amino acid sequence Gly-Ala-

Gly-Ala repeated many times, and the chains pack together as shown in the diagram. The diagram shows the R groups of the two amino acids.

Which of the following describes this structure?

A -helix held together by hydrogen bonds B -helix held together by ionic bonds C -sheet held together by hydrogen bonds D -sheet held together by ionic bonds Answer to multiple-choice test

1 A

2 C 3 A

4 C 5 B

6 C 7 A

8 B 9 D 10 C


Carbohydrates - Monosaccharaides, Disaccharides

Carbohydrates:

- Sugar polymers

- Molecules contain C, H, O atoms

- H atoms are twice as many as C or O atoms (C6H12O6)

Monosaccharides

The simplest carbohydrates

They are sugar: C = 3 = triose; C = 4 = tetrose; C = 5 = pentose; C = 6 = hexose

Examples of hexose sugars: glucose, fructose, galactose (C6H1206)

Molecules often have the form of a ring, made up of some C atoms and one

O atom.

Glucose molecules have 2 forms: -glucose and -glucose.


Disaccharides

Different disaccharides can be formed by linking different monosaccharaides. The bond that joins them together = glycosidic bond.

Condensation reactions (dehydration): 2 monosaccharaides covalently

joined; H20 is formed.


Hydrolysis reaction (splitting by water): disaccharides are split into 2 monosaccharaides by breaking the glycosidic bond; a molecule of H20 is

added.

Functions of monosaccharaides and disaccharides

Good sources of energy in living organisms, used in respiration for making ATP.

Transportable through the body because of the solubility: glucose is transported dissolved in blood plasma (animal), sucrose is transported in phloem sap (plant).

All monosaccharaides and some disaccharides are reducing sugars (reduce blue Benedict's solution to produce an orange-red precipitate). Sucrose is

a non-reducing sugar.


Carbohydrates Polysaccharides

Molecules contain hundreds/thousands of monosaccharaides linked into long

chains. Molecules are enormous --> the majority do not dissolve in water --> good for storing energy (starch and glycogen) or for forming strong

structures (cellulose).

1. Storage Polysaccharides

Glycogen (in animals and fungi) Made of -glucose molecules linked together by glycosidic bonds.

Most of the bonds are 1-4 links (C1 on one glucose + C4 on the next)

There are some 1-6 links, which form branches in the chain.

The bonds can be hydrolyzed by carbohydrase enzymes to form monosaccharaides, used in respiration.

The branches increase the rate of hydrolysis.

1-4 and 1-6 links in Glycogen.


Starch (in plants) A mixture of amylose and amylopectin. Both forms of starch are polymers of

- Glucose. Natural starches contain 10-20% amylose and 80-90% amylopectin.

Amylose molecule is a very long chain with 1-4 links. The chain coils up into a spiral, held in shape by H bonds between the glucose units.

Amylopectin differs from amylose in being highly branched. Short side chains

of about 30 glucose units are attached with 1- 6 linkages approximately every 20-30 glucose units along the chain.

2. Structural polysaccharides

Plant cell walls contain the polysaccharide cellulose:

Made of many glucose molecules, linked by 1-4 links.

Adjacent glucose molecules in the chain are upside-down to one another.


The chain is straight (not spiraling).

H bonds between chains --> very strong microfibrils --> cell wall will not

break easily if the plant cell absorbs water; difficult to digest (few organisms

have enzyme that can break the 1-4 bonds).


Tests for Carbohydrates

Tests for Reducing sugars, Non-reducing sugar and Starch.

1. Reducing sugar (Benedict's test)

All monosaccharaides and most disaccharides (except sucrose) will reduce blue CuSO4 (II), producing a precipitate of red Cu2O(I).

Benedicts reagent is an aqueous solution of CuSO4(II), Na2CO3 and sodium citrate.

2 cm test solution + 2 cm Benedicts reagent.

Shake, and heat for a few minutes at 95C in a water bath.

The mass of precipitate or intensity of the color indicates the amount of reducing sugar present ---> the test is semi-quantitative.


2. Non-reducing sugar (Benedict's test)

Principles: Sucrose is a non-reducing sugar (not reduce CuSO4)---> Benedict's test(-)

If it is hydrolyzed to form glucose and fructose ---> Benedict's test (+).

So sucrose is the only sugar that will give a (-) Benedict's test before hydrolysis

and a (+) test afterwards.

Steps:

Test a sample for reducing sugars to be sure it does not contain reducing sugars.

Boil the test solution with dilute HCl for a few minutes to hydrolyze the glycosidic bond.

Neutralize the solution by gently adding small amounts of solid NaHCO3 until it stops fizzing.

Test for reducing sugar.

3. Starch (Iodine test)

2 cm of test solution + 2 drops of iodine/KI solution.

A blue-black color indicates the presence of starch as a starch-polyiodide complex is formed.

Starch is only slightly soluble in water, but the test works well in a suspension or as a solid.


Lipids - Triglycerides and Phospholipids

Lipids:

- Include triglycerides + phospholipids.

- Molecules contain C, H, O atoms

- Very small proportion of O.

- Insoluble in water.

1. Triglycerides

- Made of glycerol 'backbone', attached to 3 fatty acids by ester bonds.

Fatty acids

Have long chains of C and H atoms.

Each C atom has 4 bonds: 2 to C atoms, 2 to H atoms.

Sometime, only 1 H atom attached --> C atom has a 'spare' bond, attached to the next-door C atom (also has 1 H bonded) ---> double bond.

Unsaturated fatty acid has 1 C-C double bonds (do not contain quite as much H).

Saturated fatty acid has no double bonds.


Lipids containing unsaturated fatty acids ---> unsaturated lipids (in plant)

Lipids containing completely saturated fatty acids ---> saturated lipids (in animal)

Unsaturated lipids tend to have lower melting points than saturated lipids.

Triglycerides are insoluble in water ---> energy storage in plants, animals and fungi. They contain

more energy per gram than polysaccharides.

A. In mammals

Triglycerides are building up beneath the skin in the form of adipose tissue:

It cells contain oil droplets of triglycerides;

Helps to insulate body against heat loss.

Relatively low density ---> buoyancy ---> useful for aquatic mammals living in cold water (whales, seals).

Forms a protective layer around organs (e.g. kidneys).


B. In plants

Triglycerides = major part of energy stores in seeds:

Cotyledons (sunflower seeds)

Endosperm (castor beans)

2. Phospholipids

Made of glycerol 'backbone', 2 fatty acids and 1 phosphate group.

Fatty acid chains are hydrophobic: no electrical charge ---> not attracted to H2O molecules.

Phosphate group is hydrophilic: has electrical charge ---> attracted to H2O molecules.

In H2O, phospholipid molecules arranges into a bilayer: hydrophilic heads facing outwards into the water + hydrophobic tails facing inwards, avoiding water.

This is the basic structure of a cell membrane.


3. Emulsion (Ethanol) test for lipids

Dissolve the substance by mixing it with absolute ethanol.

Decant the ethanol into water.

If lipids are present in the mixture, it will precipitates and forms a milky emulsion.

A milky emulsion indicates the presence of lipid.


Proteins - Amino acids, Peptide bonds

Proteins are large molecules made of long chains of amino acids.

1. Amino acids

All proteins have the same basic structure. They consist of an Amino Group

(NH2), a Carboxyl group (COOH), and a Carbon in the middle which bonds

with a Hydrogen atom and an 'R' group, which is specific to individual amino

acids.

There are 20 naturally occurring 'R' groups, making amino acids neutral, acidic,

alkaline, aromatic (has a ring structure) or sulphur-containing). The 20 R

groups correspond to 20 different amino acids. Each different amino acid has a

specific name. For example, Alanine's 'R' group consists of CH3.

2. Peptide bonds

a. Condensation reaction:

2 amino acids are joined by a peptide bond ---> dipeptide + H2O.


b. Hydrolysis reaction:

Dipeptides are split into 2 amino acids by breaking the peptide bond using a molecule of H20.


Protein- Primary, Secondary, Tertiary, Quaternary Structure

Amino acids can be linked together in any order to form a long chain -

polypeptide.

Protein molecules can be made up of the same polypeptides or different

polypeptides.

1. Primary structure: The sequence of amino acids in a polypeptide or

protein molecule.

The 3 letters in each circle are the first 3 letters of the amino acid.


2. Secondary structure: The way in which the primary structure of a

polypeptide chain folds.

After synthesis, polypeptide chains are folded or pleated into different shapes: Alpha helix (regular 3D shape) and Beta-pleated sheet (twisted,

pleated sheet)

The helix is hold by many Hydrogen bonds between amino acids at

different places in the chain, giving the shape great stability.

The typical Alpha helix is about 11 amino acids long.


3. Tertiary structure: The final 3D structure of a protein, involving

coiling or pleating of the secondary structure.

Tertiary structure.

Tertiary structure is held by:

1. Hydrogen Bonds - formed between amino acids at different points in the chain.

2. Disulphide Bonds - a strong double bond (S=S) formed between the Sulphur atoms within the Cysteine monomers.

3. Ionic Bonds - formed between 2 oppositely charged 'R' groups (+ and -) found close to each other.

4. Hydrophobic & Hydrophilic Interactions: amino acids may be hydrophobic or hydrophilic; in a water based environment, the hydrophobic parts of globular

protein are orientated towards center and the hydrophilic parts are towards edges.


4. Quaternary structure: 2 polypeptide chains join together to form a

protein.

Some proteins are made up of multiple polypeptide chains, sometimes with

an inorganic component (e.g. a haem group in haemoglogin) called a Prosthetic Group. These proteins will only be able to function if all subunits

are present.

The polypeptide chains are held by the same type of bonds as in the tertiary

structure.


The tertiary and quaternary structures of a protein, and its properties, are

determined by its primary structure.

Additional sources: Some parts of the note are taken from A level Notes.


Globular and Fibrous Proteins - Haemoglobin and Collagen

Globular and Fibrous are 2 main types of proteins with a 3D structure.

1. Haemoglobin, a globular protein

Composed of 2 + 2 polypeptide chains + 1 inorganic prosthetic Haem group.


Hb's function: carry O2 from lungs to respiring tissues.

2. Collagen - a fibrous protein

Composed of 3 polypeptide chains wound around each other. Each chain is

a coil itself of around 1000 amino acids.


Structure strength is increased by forming:

- H bonds between the 3 polypeptide chains.

- Collagen molecules wrapped around each other ---> Collagen

Fibrils

- Collagen Fibrils ---> Collagen Fibers.

Collagen's function: support and elasticity in many animal tissues (human skin, bone and

tendons).


3. Test for proteins

The Biuret Test shows the presence of peptide bonds, which are the basis for

the formation of proteins. These bonds will make the blue Biuret reagent

turn purple.

Add biuret solution. A purple color indicates the presence of protein.


Water

About 80% of the organism's body is H2O.

Its molecule has a small negative charge (-) on the O atom a small positive

charge (+) on each H atom. This is called a dipole. This makes H2O an

excellent solvent.

Hydrogen bond = attraction between (-) and (+) parts of

neighboring H2O molecules.

Solvent properties of water

The dipoles on H2O molecules make water an excellent solvent.

If you stir NaOH into H2O, the Na+ and Cl- separate and spread between the H2O molecules --> They dissolve in the water.

The Cl- is attracted to the small (+) charge on the H of H2O molecules.

The Na+ is attracted to the small (-) charge on the O of H2O molecules.


Any substance that has fairly small molecules with charges on them, or that

can separate into ions, can dissolve in water.

Being a good solvent, H2O helps:

- To transport substances around the bodies of organisms. The blood plasma

of mammals is mostly water, and carries many substances in solution: glucose,

oxygen, ions (Na...).

- To dissolve reactants ---> enable metabolic reactions.


Thermal properties of water

1. H2O is liquid at normal Earth to

The H bonds between H2O molecules prevent them flying apart at normal to.

Between 0oC and 100oC, water is in the liquid state. The H2O molecules move randomly, forming transitory H bonds with each other.

Other substances with similar molecule structure, such as hydrogen sulfide

(H2S), are gases at these to (no H bonds to attract their molecules to each other).

H2O and H2S molecules have similar structure.

2. H2O has a high latent heat of evaporation

When a liquid is heated, its molecules gain kinetic energy, moving faster +

a lot of heat energy is needed to break H bonds between water molecules. Those molecules with the most energy are able to fly off into the

air.

When H2O evaporates, it absorbs a lot of heat from its surroundings --->

The evaporation of H2O from the skin of mammals when they sweat and the

transpiration from plant leaves has a cooling effect.

3. H2O has a high specific heat capacity

Specific heat capacity is the amount of heat energy that has to be added

to a given mass of a substance to raise its to by 1oC.

The higher the kinetic energy the higher the to: a lot of energy is needed to rise to (to speed of H2O molecules + break H bonds) ==> Bodies of H2O

(oceans, lake) do not change to as easily as air does. Bodies of organisms (with large amounts of H2O) do not change to easily.


4. H2O freezes from the top down

Most substances are denser in solid form than liquid form and will sink if submerged in their liquid state. But H2O is LESS dense in its solid state, and

will float. This has to do with the crystal structure of ice.

When water cools (to) the density of water (molecules lose kinetic energy, getting closer).

Below 4C this trend is reversed: When H2O approaches freezing point, molecules form a lattice and stretches its very elastic H bonds --> density

(lower than density at 4C) --> Ice floats on water.

The layer of ice acts as an insulator, slowing down the loss of heat

from H2O beneath it, which tends to remain at 4C.

The H2O under the ice remains liquid, allowing organisms to continue to live in it

even when air temperatures are below the freezing point of H2O.


Inorganic ions

Biological Molecules (AS level Bio)

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