3.1 Biological molecules

What is maltose made of?

Two alpha-glucose molecules

What is sucrose made of?

One glucose and one fructose molecule

What is lactose made of?

One glucose and one galactose molecule

What is the difference between starch, glycogen and cellulose?

Starch and glycogen have alpha-glucose while cellulose has beta-glucose

How is the structure of starch linked to function?

Amylose (1-4 linkage) is coiled and helical so compact.

Amylopectin (1-6 linkage) is branched so more able to hydrolyse for respiration.

Insoluble so doesn’t affect water potential and large so doesn’t leave cells which relates to function of energy store in plants.

How is the structure of glycogen linked to function?

It is compact and more branched so can be broken down quickly (energy store of glucose in the liver and muscles).

Insoluble, helical and large.

How is the structure of cellulose linked to function?

Straight chains of beta-glucose monomers are linked by many unbranched hydrogen bonds forming fibrils and providing strength in cell walls to maintain turgidity.

What are examples of reducing sugars and how do you test for them?

Glucose, fructose, lactose, maltose.

1. Add Benedict’s reagent (blue) and heat

2. Positive result= brick-red precipitate

What is an example of a non-reducing sugar and how do you test for it?

Sucrose

1. Ensure negative result for reducing sugar test.

2. Add HCl and boil, then add sodium hydrogencarbonate.

3. Add Benedict’s and heat

4. Positive result= brick-red precipitate

What is the test for starch?

1. Add iodine solution (orange)

2. Positive result= blue-black

Roles of lipids in the body

Energy store, energy source, insulation, buoyancy, waterproofing, cell membranes (phospholipid), protection of vital organs

What are similarities and differences between triglycerides and phospholipids?

Similarities: formed via condensation reactions, contain glycerol and at least 2 fatty acids

Differences: phospholipid= 2 fatty acids, has phosphate, polar; triglyceride= 3 fatty acids, no phosphate, non-polar

What is the biochemical test for lipids?

1. Add ethanol to sample and shake

2. Add water and shake

3. Positive result= cloudy-white emulsion

What is an example of proteins functioning as enzymes?

Protease

What is an example of proteins functioning as transport?

Haemoglobin

What is an example of proteins functioning as movement?

Actin/myosin

What is an example of proteins functioning as cell recognition?

Antigens

What is an example of proteins functioning as channels?

Membrane proteins

What is an example of proteins functioning as structure?

Collagen/ keratin/ elastin

What is an example of proteins functioning as hormones?

Insulin

What is an example of proteins functioning as protection

Antibodies

What is the bond between amino acids?

Peptide bond

Describe the primary structure of a protein

Specific sequence of amino acids in the polypeptide chain.

Involves peptide bonds.

Different proteins have different primary structures, giving different properties.

Describe the secondary structure of a protein

Folding of the amino acid chain into alpha-helices or beta-pleated-sheets.

Involves hydrogen bonds between the C=O and -NH of the linked amino acids.

Describe the tertiary structure of a protein

Bonding between R-groups gives rise to a 3D shape.

Involves hydrogen and ionic bonds and disulfide bridges.

Describe the quaternary structure of a protein

Protein with more than one polypeptide chain eg. haemoglobin, antibodies

What is the biochemical test for proteins?

Add Biuret solution.

Positive result= blue to purple

How do enzymes work?

1. Lower activation energy

2. Increase number of successful collisions taking place

3. Formation of an enzyme-substrate complex causes bonds to form/break in substrate

4. Provides alternative chemical pathway

What is the induced-fit hypothesis of enzyme action?

Binding of the substrate to the enzyme causes the enzyme’s active site to change shape to fit around the substrate and become complementary

How does denaturation affect enzyme action?

pH and temperature affect the bonds in the tertiary structure of the enzyme. The substrate can no longer bond as the active site is changed.

What is the effect of temperature on enzyme activity?

• Enzyme activity increases as temperature increases because there is increased kinetic energy so more collisions with sufficient energy therefore it is more likely for enzyme-substrate complexes to form

• The optimum temperature is around 37^oC

• After the optimum temperature, tertiary and quaternary bonding is disrupted and the enzyme active site is altered, so enzyme-substrate complexes can no longer form

What is the effect of pH on enzyme activity?

• At low pHs, the enzyme is denatured as H⁺ ions (acid) disrupt ionic bonds at the active site

• optimum pH

• at high pHs, the tertiary and quaternary bonding is disrupted and the active site altered, so enzyme-substrate complexes can no longer form

What is the effect of substrate concentration on enzyme activity?

• Until the saturation point, not all active sites are occupied and substrate concentration is the limiting factor. Therefore enzyme activity increases as substrate concentration increases because more enzyme-substrate complexes can form (more frequent collisions increases the chance of successful collisions)

• After the saturation point, all active sites are occupied and enzyme concentration is the limiting factor. Enzyme activity is constant because no more enzyme-substrate complexes can form.

What is a competitive inhibitor?

• They compete with the substrate for the active site (bind in place of substrate)

• e.g methanol

• Similar shape to substrate; complementary to active site

• Does not bind permanently or damage active site

What does a graph look like with a competitive inhibitor?

• ROR decreases as active sites are occupied so fewer available for substrate to bind

• The effect of the inhibitor is reduced at high concentrations as the substrate competes more effectively with the inhibitor therefore there is a greater frequency of successful collisions

What is a non-competitive inhibitor?

• It binds to a site other than the active site (allosteric site)

• e.g mercury, lead, arsenic

• Changes tertiary structure of active site so substrate is not complementary and can no longer bind

• May remain permanently attached, destroying enzyme

How does increasing substrate concentration affect the ROR with non-competitive inhibitors?

Increasing the amount of substrate has no effect as the enzyme is destroyed

What is DNA (deoxyribonucleic acid) made up of?

Two polynucleotide strands that are twisted around each other in a double helix

What does a DNA nucleotide consist of?

The pentose sugar deoxyribose, a phosphate group and one of four nitrogenous bases: cytosine, adenine, guanine and thymine

What is a polynucleotide made up of?

Many nucleotides joined by condensation reactions forming phosphodiester bonds

What are the complementary base pairing rules?

Cytosine/guanine (3 H bonds)

Adenine/thymine (2 H bonds)

Which bases are purines and which are pyrimidines?

Purines (larger)= adenine and guanine

Pyrimidines (smaller)= cytosine and thymine

How was the structure of DNA discovered?

Watson and Crick- first proposed double helix structure

Rosalind Franklin and Maurice Wilkins- X-ray crystallography proved double helix structure

Erwin Chargaff- discovered percentages of bases which showed which ones paired up

What is the function of DNA?

• stores genetic information

• copies/replicates genetic information

• codes for polypeptides

How is the structure of DNA related to its function?

• long molecule: able to copy/replicate genetic information, stores a large amount of genetic information

• sugar-phosphate backbone: provides strength and stability, protects bases and maintains base sequence

• bases in sequence: stores genetic information, 3 bases code for one amino acid (determines primary structure of proteins)

• double-stranded with complementary base pairing: allows information to be replicated/transcribes, one strand acts as a template for the other strand or RNA in transcription

• weak hydrogen bonds between base pairs: able to ‘unzip’ so it can be copied and replicated (transcription)

• helical structure: coiled so compact

Describe the semi-conservative replication of DNA

1. Hydrogen bonds between bases broken. Catalysed by DNA helicase

2. Free nucleotides are attracted to their complementary bases. Complementary base pairing occurs. Each strand acts as a template to form a copy of the other strand

3. DNA polymerase forms phosphodiester bonds between adjacent nucleotides

4. Two identical double helices are formed. Each has one original strand and one new strand

What is the structure of an RNA nucleotide?

Ribose attached to phosphate group and adenine, cytosine, guanine or uracil

What are differences between DNA and RNA?

• DNA has deoxyribose whereas RNA has ribose

• DNA has thymine whereas RNA has uracil

• DNA is long whereas RNA is short

• DNA is a double helix whereas RNA is a single strand

Describe tRNA

• ribose sugar

• adenine, guanine, cytosine and uracil

• single-stranded

• 80 nucleotides in strand

• has sections of hydrogen bonding

What is the structure of ATP?

Ribose attached to adenine and 3 phosphate groups

How is energy released using ATP?

ATP + H₂O → ADP + inorganic phosphate + energy

• hydrolysis reaction

• catalysed by ATP hydrolase

How is energy stored using ADP?

ADP + inorganic phosphate + energy → ATP + H₂O

• condensation reaction

• catalysed by ATP synthase

What is ATP a source of energy for?

• movement (muscle contraction)

• photosynthesis

• glycolysis in respiration

• active transport

• co-transport

• protein synthesis (forming peptide bonds)

• exocytosis

What are useful features of ATP and why is it a more suitable energy source than glucose?

• inorganic phosphate released can be used to phosphorylate other compounds

• Releases energy on breakdown

• Uses energy from other reactions to form

• Can be readily stored/moved/broken down when needed

• Allows energy to be released in suitable amounts

What are important properties of water?

• metabolite in metabolic reactions including condensation and hydrolysis reactions- eg conversions between ADP and ATP, forming and breaking down disaccharides

• Solvent in which metabolic reactions occur- eg ions (nervous system, digestive system, kidney reabsorption), minerals in xylem of plants, translocation, blood

• High heat capacity so buffers changes in temperature- means the ocean takes a long time to be heated and cooled so temperature changes are less extreme therefore aquatic animals can survive

• Large latent heat of vaporisation, providing a cooling effect with little loss of water through evaporation

• Strong cohesion between water molecules- supports columns of water in the tube-like transport cells of plants and produces surface tension where water meets air

What are the roles of ions in pH, haemoglobin, co-transport of glucose and amino acids, components of DNA and ATP?

• pH: H⁺ ions

• Haemoglobin: Fe²⁺ ions

• Co-transport of glucose and amino acids: Na⁺ ions

• Components of DNA and ATP: PO₄^3- ions

What is the equation for pH?

pH= -log₁₀[H⁺]