Biology - Aspects of Biochemistry (Module 1)

Uses of Water

-To transport materials through the body of many organisms.

-Mot cells have 70-90 percent water; it is important for dissolving chemicals for metabolic reactions.

-Prevents overheating through evaporation during sweating.

-It is a lubricant; alveoli of lungs are kept moist to allow diffusion of oxygen.

Properties of Water

-High latent heat of vaporization (Evaporation of water requires a great deal of heat energy) and fusion (A lot of heat must be removed for water to freeze).

-High specific heat capacity

-Ice is less dense than liquid water. (water has its maximum density at 4 degrees C)

-Water has low viscosity; it is able to flow easily.

Carbohydrates formula

C_xH₂O_y (x=y)

Uses of Carbohydrates

main constituent of plants and providing structure and support- cellulose

means of storing energy - glycogen and starch

main substrate for respiration in both plants and animals - glucose

Characteristics of monosaccharides

They are sweet tasting

They are soluble in water

General formula is (CH₂O)_n where n can be any number from 3 to 7

Monosaccharides are named according to the number of carbon atoms they contain. 

Types of monosaccharides

an aldehyde group - CHO making that monosaccharide an aldose sugar

a ketone group - C=O making that monosaccharide a ketose sugar

Where is the functional group on glucose?

Glucose contains an aldehyde functional group on carbon 1.  This makes glucose an aldose sugar.  

What is the difference between alpha and beta glucose?

In alpha glucose, the hydroxyl group is at the bottom of carbon 1.  In beta glucose, the hydroxyl group is at the top of carbon 1. 

What is a pyranose ring?

A six sided ring structure formed by hexoses when the carbon atom labelled 1 combines with the oxygen on the carbon labelled 5.

How does the structure of glucose suit its function?

-Glucose contains several high energy C-H bonds. During respiration, C-H bonds are broken to release energy used to form ATP.

-The presence of the aldehyde functional group increases the reactivity of glucose allowing it to readily take part in reactions like respiration.

-Glucose is a very small molecule that can easily travel through the cell membrane to enter cells and pass through the mitochondria where respiration occurs.

Characteristics of disaccharides

-Disaccharides are sweet tasting

-Disaccharides are polar molecules and so they are soluble in water

-Some disaccharides are reducing sugars and some disaccharides are non reducing sugars.

How are disaccharides formed?

Two sugar units bond together by a covalent bond called a glycosidic bond.

Why is a glycosidic bond a condensation reaction?

When two monosaccharides bind together to form the glycosidic bond, a molecule of water is removed and so it is known as a condensation reaction.

Reducing v Non reducing Sugars

Due to the presence of either an aldehyde or ketone functional group, sulphate, which is blue in colour is reduced to an insoluble precipitate of copper oxide, which is red in colour.

-Some disaccharides, like sucrose, form non-reducing sugars because both functional groups on each of its monomers are involved in the formation of the glycosidic bond so, not available to reduce copper sulphate in Benedict's solution.

-Maltose is a reducing sugar because the aldehyde group on the 2nd glucose molecule is able to reduce copper II sulphate.

How does the structure of disaccharides suit their function?

-Disaccharides have large numbers of C-H bonds that can be easily broken down to release energy.

-Disaccharides, like sucrose, is the form in which carbohydrates are transported within the phloem of plants. Any glucose made during photosynthesis is converted to sucrose for transport.  Sucrose is less reactive (non-reducing) and so can be transported without affecting any reactions taking place within the plant cell.

What are polysaccharides?

Polymers (large molecule made up of repeating sub-units) formed from combining together many monosaccharide units joined by glycosidic bonds that are formed by condensation reactions.  The resulting chain may vary in length and be branched or folded in various ways.

Characteristics of polysaccharides

-Polysaccharides are NOT sweet tasting

-They are not soluble in water

-They are macromolecules (large molecules)

Starch

Starch is an energy storage polysaccharide found in plants.  Starch is stored in the form of granules or grains. Starch is actually made up of two different polysaccharides, amylose and amylopectin.  The percentage of each type varies according to the source of the starch but it is usually about 70 to 80% amylopectin and only 20% to 30% amylose.

Explain the structure of amylose.

-Amylose is made up of between 200-5000 alpha glucose molecules bonded together by 1,4 glycosidic bonds.

-As bonds are created, a long curled chain forms.

Explain the structure of amylopectin.

-Made up of 5000-100 000 alpha glucose molecules bonded together by 1,4 glycosidic bonds.

-Shorter chains with slight curling form with branching of glucose chains created by the formation of 1,6 glycosidic bonds.

Structure of Glycogen

-Alpha glucose molecules bind to form short chains with slight curling, held by 1,4 glycosidic bonds with branching created by 1,6 glycosidic bonds.

-Glycogen differs from amylopectin by having shorter chains but much more highly branched.

How does the structure of starch (amylose and amylopectin) and glycogen suit their energy storage function?

• These polysaccharides are insoluble and so they can be stored in the cells without having an osmotic effect on the cells.  If it were soluble, water will be drawn into the cells by osmosis.

• Being insoluble, it can be stored without easily diffusing out of the cells.

• Curling and branching makes the polysaccharides more compact and so a lot of it can be stored in a small space.

• The branches create many regions where individual glucose molecules can be removed when needed for respiration. 

Structure of Cellulose

-Cellulose is made up of straight chains of between 2000 and 3000 beta glucose molecules bonded together by 1,4 glycosidic bonds. 

-Many of these cellulose chains run parallel to each other and bundle together to form microfibrils.  The cellulose chains are held together by the formation of many hydrogen bonds which form cross-linkages.  Hydrogen bonds are relatively weak but since there are so many, collectively the chains are held quite tightly together. 

-The strength of cellulose is further increased as microfibrils are arranged in parallel groups to form fibres.  These fibres then arrange themselves in a criss-cross pattern similar to a woven basket to ensure strength. 

How do beta glucose molecules form 1,4 glycosidic bonds?

In order to facilitate hydroxyl groups aligning themselves side by side to form the glycosidic bonds between the beta glucose molecules, each beta glucose molecule must be rotated by 180^o compared to its neighbour.

How does the structure of cellulose suit its function?

Cellulose has a high tensile strength.  The tensile strength is increased when cellulose chains bundle to form microfibrils and these microfibrils bundle to form fibres.  It also increases due to the formation of many hydrogen bonds forming cross linkages holding the cellulose chains together in the microfibril.  The rotation of every other beta glucose molecule in the cellulose chain helps form many projecting OH groups on both sides of each chain so that when chains come together, OH groups are close together and form these hydrogen bonds.  The criss-cross pattern that the fibres make also contribute to cellulose's strength. 

General Characteristics of Lipids

-Made up of carbon, hydrogen and oxygen (like carbohydrates) but contain significantly less oxygen.

-Insoluble in water but soluble in organic solvents like alcohol.

-Micro molecules NOT polymers

Structure of Triglycerides

-Contains glycerol and 3 fatty acids

-Held together by ester bonds

-Fatty acids consists of a carboxylic head and a long hydrocarbon tail.

Saturated Fatty acids

-Only single bonds exist between the carbon atoms on the hydrocarbon tail. This means that the maximum number of hydrogens are present in the tail. It is therefore said to be saturated (with hydrogen).

Unsaturated fatty acids

Double bonds exist between the carbon atoms on the hydrocarbon tail.

A single double bond is a monounsaturated fatty acid ; more then one double bond is a polyunsaturated fatty acid.

Fats and Oils

Fats and oils differ structurally only because of  the presence or absence of these double bonds.  Double bonds make fatty acids and the lipids that contain them melt more easily as their melting point is lowered.  Therefore lipids containing double bonds are liquid at room temperature forming oils and lipids with no double bonds are solid at room temperature forming fats.

How does structure of triglycerides suit function?

The main function of triglycerides is to act as a long term energy store of plants and animals.  Lipids like fats and oils contain more energy per mass than carbohydrates.  Whereas 1 gram of carbohydrates contain 17 kilojoules of energy, lipids contain 38 kilojoules of energy for the same 1 gram(more high energy C-H bonds).  This makes fats and oils more efficient storage molecules because more energy can be stored for the same mass. 

-This allows organisms that move around to be lighter, still storing a considerable amount of energy.

-Also, being non polar and hydrophobic, fats and oils are insoluble in water and so will not be easily leak  ed out from cells that store it. 

Other functions of triglycerides

Insulation

In addition to storing energy long term, animals use fat as a source of insulation.  Fats are slow conductors of heat and so are often stored beneath the body surface in endothermic (maintaining a constant body temperature) animals, which help retain body heat.

Protection

Fat is often stored around delicate organs such as the kidney, where it acts as a packing material protecting the organ from physical damage.

Buoyancy

Lipids are less dense than water and so aquatic animals that have fat for insulation have the added advantage of being more buoyant.

Structure of phospholipids

-Phospholipids are structurally similar to lipids except that one of the three  fatty acids is replaced by a phosphate molecule. 

-Phospholipids are a very important component of cell membranes.  Both the inside of a cell and the environment outside the cell contains a large percentage of water.  To cope with a watery medium both inside and outside a cell, the phospholipids form a double layer (bilayer) where the hydrophilic heads of the molecules point to either the watery environment outside the cell or the watery medium inside the cells.  The hydrophobic tails point inwards shielded by the polar heads on either side.

General Properties of proteins

1.     Proteins form about 2/3 of the total dry mass of a cell.

2.      They are macromolecules.

3.     In addition to containing the atoms hydrogen, oxygen and carbon, proteins always contain nitrogen.  Sulphur is usually present, as well as, phosphorous.

4.     They are not truly soluble but form colloidal suspensions.

5.     There is an infinite number of proteins specific to each species.

6.     Proteins are built up from a linear sequence of building blocks called amino acids.

Structure of an amino acid

1.     An amino group NH₂ which is basic.

2.     A carboxyl group COOH which is acidic

3.     A hydrogen atom

4.     An R group which is a variety of different chemical groups specific to each type of amino acid.

Why is the amino acid amphoteric?

Since the carboxyl group of an amino acid is acidic and the amino group is basic, an amino acid is described as amphoteric (a substance that is both an acid and a base).  

Formation of peptide bonds

Amino acids join to one other by a condensation reaction.  The amino group of one amino acid molecule reactions with the carboxyl group of another amino acid and water is eliminated. 

-When two amino acids are joined, a dipeptide is formed.  If many amino acids join, a polypeptide is formed.

Hydrogen bonds

-Results from the attraction between the electronegative oxygen atoms on the CO groups and the electropositive H atoms on the OH or NH groups.

-weak bonds which can be broken by high temperatures and pH changes.

Ionic bonds

-Occur between any ionized amino group and carboxyl group that has not been involved in forming peptide bonds.  They can occur at the ends of any polypeptide chain and additional ionized carboxyl and amino groups of R groups.

-Stronger than hydrogen bonds.  They can be broken by pH changes.

Disulphide bridges

-Occur between the sulfur atoms of two cysteine amino acids.

-Very strong covalent bonds which makes the protein structure very stable.  These bonds can be broken by reducing agents.

Hydrophobic interactions

Occur between non polar R groups with many hydrocarbons present. These R groups repel water and so cause the polypeptide chain to fold or twist as they take up a position towards the center of the protein away from the watery medium outside.

-Hydrophobic interactions are very weak.

Primary structure of proteins

The primary structure of a protein molecule is the types of amino acids contained in a polypeptide chain and the specific sequence in which they are joined.  Peptide bonds hold a protein in its primary structure. 

P = Aⁿ   

Secondary Structure of proteins

-The secondary structure of a protein is created when R groups of amino acids within a polypeptide chain form hydrogen bonds and cause the chain to fold or twist in specific ways.

i.       α-helix – the polypeptide chain is coiled into a cylindrical shape due to hydrogen bonds forming between oxygen of the COO group of one amino acid and the hydrogen of the NH group of the amino acid four places ahead of it.

ii.      β-pleated sheet – the polypeptide chains are linked in parallel flat sheets formed by hydrogen bonds  between NH and CO groups of adjacent chains. 

Tertiary structure

The tertiary structure of a protein is created when the secondary protein structure is. twisted and folded even further creating a complex and unique structure.  This is a result of all four possible bonds mentioned before that occur when R groups interact. 

Quaternary structure

-The association of two or more polypeptide chains to form a large complex protein structure is called the quaternary structure of the protein.  All four bonds holding a protein in its tertiary structure also hold a protein in its quaternary structure.

-A large complex protein may also include non-protein components called prosthetic groups.  The haem groups attached to the protein haemoglobin is an example of a non-protein or prosthetic group.

Fibrous Proteins

-        Form long polypeptide chains that run parallel to each other

-        Have polypeptide chains with a repeated sequence of amino acids

-        Have chains that are held together by cross-linkages

-        Are extremely strong and stable

-        Are insoluble in water

-        Have a structural function

example: Collagen fibres making up tendons, skin, cartilage, bones, teeth and walls of blood vessels.

 Myosin of muscle

Keratin of hair

Collagen

Collagen molecules consist of 3 polypeptide chains wound together in a helix.  The chains are held together in the helix by many hydrogen bonds.  Each chain consist of amino acids in the repeated sequence glycine – proline – alanine.  Thousands of these collagen molecules run parallel to each other to form collagen fibres.  Fibres are held together by cross-linkages consisting of covalent bonds between lysine amino acids of adjacent fibres.

Globular Proteins

-        Form a compact ball-shaped structure

-        Have a varied amino acid sequence that is specific to the structure

-        Have a relatively unstable structure

-        Are water-soluble because they curl up into a ball shape where hydrophobic R groups point to the centre and hydrophilic R groups point towards the outside.

-        They have a metabolic function.

example: Enzymes, Antibodies, Hormones

Transport pigments like haemoglobin and myoglobin

Haemoglobin

Haemoglobin (Hb) has a quaternary structure. Each molecule of haemoglobin consisting of 4 polypeptide chains, two α polypeptide chains 141 amino acids long and two β polypeptide chains 146 amino acids long.  Each chain curls up into a compact shape and all four chains  are linked to form a compact spherical Hb molecule.  Hydrophobic interactions help Hb to be soluble as hydrophilic amino acids orient themselves to point outwards.  Each polypeptide chain has a haem group associated with it.  At the centre of each haem group is a ferrous iron where one molecule of oxygen binds to form oxyhaemoglobin.