Biology 2.1.2- Biological Molecules

What are the 4 main biological roles of water?

• Habitat

• Solvent

• Coolant

• Transport medium

Why is water a polar molecule?

• The oxygen atom attracts the electrons more strongly than the hydrogen atoms

• This gives the oxygen a weak negative charge (δ^-) and the hydrogen a weak positive charge (δ⁺)

• This means water has a dipole

How do hydrogen bonds work in water and why are they useful?

• Weak hydrogen bonds form between the hydrogen and oxygen atoms of adjacent water molecules, due to it’s polarity

This means that water:

• Is a good solvent as it attracts other polar molecules

• Has a high specific heat capacity + latent heat of vaporisation

• Is less dense when it freezes

• Has a high cohesion to itself and high surface tension

How do the properties of water relate to it’s role as a solvent, and what are the examples of it?

• Water is a polar molecule, so it attracts other polar molecules and dissolves them

• Eg. Water can carry mineral ions in plant xylem + blood plasma carries blood cells and other substances

How do the properties of water relate to it’s role as a coolant, and what are the examples of it?

• Water has a high specific heat capacity, so it can take in a lot of energy before changing temperature

• It also has a high latent heat of vaporisation, so it takes in a lot of energy when boiling

• Eg. Evaporation is used to cool down, by sweating or panting

How do the properties of water relate to it’s role as a habitat, and what are the examples of it?

• Water has a high specific heat capacity, so it can take in a lot of energy before changing temperature

• Freezes in a crystalline structure, so it is less dense when solid, meaning ice floats and can insulate water bodies

• Polar molecule, so it attracts other polar molecules and can dissolve them

• Eg. Creates a stable environment in ponds, with a constant temperature (for enzyme activity) and dissolved nutrients

How do the properties of water relate to it’s role as a transport molecule, and what are the examples of it?

• Water is a polar molecule, so it attracts other polar molecules and can dissolve them

• This also means it has high cohesion to itself and adhesion to surfaces, so can easily flow

• Eg. Water can carry mineral ions in plant xylem + blood plasma carries cells and dissolved substances

What chemical elements make up carbohydrates, lipids, proteins and nucleic acids?

Carbohydrates = C, H and O

Lipids = C, H and O (+ P for phospholipids)

Proteins = C, H, O and N (+ P and S sometimes)

Nucleic acids = C, H, O, N and P

What are the biological cations calcium, sodium, potassium, hydrogen and ammonium each used for?

Calcium (Ca 2+) - nerve impulses and muscle contractions

Sodium (Na +) - nerve impulses, transport of substances across cell membranes and kidney function

Potassium (K +) - nerve impulses, kidney function and stomata

Hydrogen (H +) - catalysts and pH determination

Ammonium (NH4 +) - used in protein synthesis

What are the biological anions nitrate, hydrogen carbonate, chloride, phosphate and hydroxide each used for?

Nitrate (NO3 -) - amino acid formation

Hydrogen carbonate (HCO3 -) - maintains blood pH

Chloride (Cl -) - balance sodium and potassium ions in cells and maintains blood pH

Phosphate (PO4 3-) - cell membranes, bone formation, and is a component of DNA, RNA and ATP

Hydroxide (OH -) - catalysts and pH determination

What are the structures of alpha and beta glucose?

Glucose is a hexose sugar with two isomers- they both have the formula C6H12O6

What are the structures of ribose and deoxyribose?

Ribose and deoxyribose are pentose (5 carbon) sugars, with similar formulas except that deoxyribose has one less oxygen than ribose (lost from the second carbon)

What three properties do monosaccharides have in common?

• Soluble in water

• Sweet tasting

• Forms crystals

How can disaccharides and polysaccharides be formed and broken down?

They can be formed by condensation reactions- when two hydroxyl (OH) groups from different saccharides interact to produce a water molecule and a glycosidic bond between the two saccharides

• This can be catalysed by enzymes

They can be broken down by hydrolysis- when water is added to a di or polysaccharide, breaking the glycosidic bond to form a hydroxyl group on each saccharide

• This can be catalysed by (different) enzymes

• We use this to test for non reducing sugars

What are the three most common disaccharides made from?

Maltose- two glucose molecules

Sucrose- glucose + fructose

Lactose- glucose + galactose

What are reducing sugars?

Reducing sugars can give away electrons via the oxidisation of a carbonyl (C=O) group

• This is why reducing sugars can be detected using Benedict’s solution- they reduce the soluble blue copper sulphate to insoluble brick-red copper oxide

• All monosaccharides and some disaccharides are reducing sugars- polysaccharides aren’t

How can we detect non-reducing sugars and why?

Non-reducing sugars (di or poly saccharides) must be broken down into their monosaccharides, which are always reducing sugars, to be detected using Benedict’s solution

• We do this by hydrolysis, where we heat the sample with hydrochloric acid to break the glycosidic bond, and then neutralise it

• Then we can test with Benedict’s solution to see whether reducing sugars were produced, and hence whether non reducing sugars were originally present

What is the structure of starch?

Starch is made from two different alpha glucose structures :

• Amylose (20%)- a straight chain linked by 1,4-glycosidic bonds- amylose curls into a helix shape which allows it to be more compact

• Amylopectin (80%)- a branched chain linked by 1,4 and 1,6-glycosidic bonds

What is starch used for and how is it well suited?

• Starch is the main carbohydrate store in plants

• Stored in the plastids- amyloplasts and chloroplasts

This because it is:

• Compact, so large quantities can be stored

• Insoluble, so it won’t change the water concentration in cells and affect osmosis

• Amylopectin (80%) is linked by some 1,6-glycosidic bonds, so it has many terminal glucose molecules that can be hydrolysed for respiration or added for storage

What is the structure of glycogen?

• Made up of alpha glucose molecules linked by 1,6 and 1,4-glycosidic bonds

• Glycogen has a similar structure to amylopectin but is more branched, because it has more 1,6-bonds

What is glycogen used for and how is it well suited?

• Glycogen is used for storage in animals

• Stored in liver and muscle cells

This because it is:

• Compact but relatively large, so large quantities can be stored (more 1,6-bonds means it is more compact than amylopectin)

• Insoluble, so it won’t change the water concentration in cells and affect osmosis

• Linked by many 1,6-glycosidic bonds so it has many terminal glucose molecules that can be hydrolysed for respiration or added for storage

What is the structure of cellulose?

• Made up of beta glucose molecules linked by 1,4-glycosidic bonds

• To bond together, every other beta glucose molecule is flipped

• This means that hydrogen bonds can form between strands, to create microfibrils

• These make up the cellulose fibres that link into a network

What is cellulose used for and how is it well suited?

• Cellulose makes up the majority of plant cell walls

This is because it is:

• Held together by many hydrogen bonds between strands, so it has a very high tensile strength and is able to withstand the pressure from turgidity of the cell

• Linked to other molecules like lignin, which increases the strength of the cell walls

• Permeable, so water and solutes can enter or leave the cell

What are triglycerides?

• Triglycerides are lipids made up of a glycerol backbone bonded with three fatty acid chains

• The three hydroxyl groups on glycerol and the carboxyl group on each fatty acid go through a condensation reaction to create ester bonds (process of esterification)

How can triglycerides differ in structure?

• Fatty acids can differ in length

• Fatty acids can be saturated (all single bonds) or unsaturated (containing a double bond)

• A mono-unsaturated fatty acid has one double bond, while a poly-unsaturated one has multiple

The double bonds in an unsaturated fatty acid cause the molecule to bend, so they can’t pack together as closely, and they are liquids (oils)

What are phospholipids?

• Phospholipids are lipids made up of a glycerol backbone joined to two fatty acids and a phosphate group

• The phosphate group is polar, so it is hydrophilic (attracted to water and aqueous solutions)

• Whereas the fatty acids are non-polar and hydrophobic

• This allows phospholipids to form cell membranes

How do the properties of triglycerides relate to their function?

Triglycerides are mainly used as energy storage molecules, because:

• They’re insoluble, so they don’t affect osmosis in cells and can be stored in large quantities

• The long fatty acid chains contain lots of chemical energy (more than carbohydrates) so triglycerides can store energy and release it when broken down

  • Plants mostly store unsaturated fats, while animals saturated fats

  • Triglycerides are also used to insulate nerve fibres in the myelin sheath and insulate animals against heat loss (as part of the adipose tissue layer), provide buoyancy and protect organs

How do the properties of phospholipids relate to their function?

Phospholipids make up cell membranes, because:

• The phosphate group is hydrophilic and the fatty acids are hydrophobic, so they can form a bilayer with the phosphate groups facing aqueous solution and the fatty acids in the middle

• This allows cells to regulate the concentration of substances and compartmentalise organelles, improving efficiency

How do the properties of cholesterol relate to it’s function?

Cholesterol strengthens and stabilises the phospholipid membrane, because:

• They are small and flat molecules, so can fit between phospholipid molecules

• They bond to the hydrophobic fatty acids, packing the phospholipids in more closely and rigidly- this decreases the fluidity of the cell membrane

  • Cholesterol is only found in animal cell membranes

What is the structure of amino acids?

There are 20 amino acids found in proteins- these differ by having different R groups

How are dipeptides and polypeptides formed?

A peptide bond between two amino acids is formed through condensation- when the OH from the carboxyl group of one amino acid reacts with an H from the amine group of another amino acid

• Peptide bonds are covalent

This is reversed by a hydrolysis reaction

What are the levels of protein structure?

Primary- the sequence of amino acids in the polypeptide chain

Secondary- how hydrogen bonds between amine groups and carboxyl groups cause the chain to fold into a beta pleated sheet or coil into an alpha helix

Tertiary- hydrophilic/phobic interactions, hydrogen bonds, ionic bonds and disulphide bonds hold the R groups together into a complicated shape

Quaternary- multiple polypeptide chains (subunits) joined together, eg. in haemoglobin

Compare the strengths of different bonds within the tertiary structure of a protein

Strongest- disulphide bridges + ionic bonds

Middle- hydrogen bonds

Weakest- hydrophobic + hydrophilic interactions

Describe the structure and function of globular proteins

• Globular proteins form a spherical shape because their hydrophobic R groups are orientated towards the centre of the protein but their hydrophilic R groups are positioned on the outside of the protein

• This means that most globular proteins are soluble

• The amount of possible tertiary structures of globular proteins gives them very specific shapes (beneficial for enzymes and antibodies)

• Globular proteins can be conjugated by containing a prosthetic group eg. haemoglobin

Globular proteins are transport molecules, enzymes, and hormones

Describe an example of each of the three functions of globular proteins

Haemoglobin is a transport molecule found in red blood cells

• It is made up of four polypeptide chains and four prosthetic haem groups (it is a conjugated protein), which are able to temporarily bond to oxygen

• Oxygen is not very soluble in water but haemoglobin is soluble, so it allows oxygen to be carried more efficiently around the body for respiration

Enzymes, eg. amylase and catalase, are biological catalysts that speed up reactions in the body

• There are many possible structures of globular proteins due to bonding between R groups, which allows enzymes to have very specifically shaped active sites complementary to their function

Insulin is a hormone involved in the regulation of blood glucose concentration

• Hormones are transported in the bloodstream so they need to be soluble

• Hormones have to have a specific shape to activate receptors, which is possible due to the variations in globular protein structure

Describe the structure and function of fibrous proteins

• Fibrous proteins are made up of parallel polypeptide chains held together by cross links, forming long, rope-like fibres

• They have many hydrophobic R groups, making them insoluble

• Fibrous proteins have a limited number of amino acids with the sequence usually being highly repetitive

• This forms organised structures that are very strong

Fibrous proteins are used as structural components

Describe the three main fibrous proteins

Keratin is found in hair, skin and nails

• It contains lots of disulphide bridges, which makes it strong, inflexible and insoluble

Elastin is found in elastic fibres like the walls of blood vessels and the skin

• It is a quaternary protein made from chains of a stretchy polypeptide, which makes it insoluble, stable and elastic

Collagen is a structural protein forming connective tissues

• Collagen molecules have a triple helix structure held together by hydrogen bonds, giving it a high tensile strength