Section 1: Biological Molecules

What are monomers?

Smaller units from which larger molecules are made

What are polymers?

Molecules made from a large number of monomers joined together

Examples of monomers

Monosaccharides, amino acids and nucleotides

What is a condensation reaction?

chemical reaction which results in the formation of a bond between 2 molecules and the elimination of a water molecule

What is a monosaccharide?

The monomers from which larger carbohydrates are made

Examples of monosaccharides

glucose, galactose, fructose

What is a glycosidic bond?

A bond formed in a condensation reaction between 2 monosaccharides

What is a hydrolysis reaction?

a reaction in which a bond is broken between 2 molecules and involves the use of a water molecule

What is a dissaccharide?

Molecule formed from the condensation of 2 monosaccharides

What is maltose?

Disaccharide of glucose + glucose

What is sucrose?

Disaccharide of glucose + fructose

What is lactose?

Disaccharide of glucose + galactose

What are the isomers of glucose?

alpha glucose and beta glucose

What is a polysaccharide?

a complex carbohydrates that is made up of more than two monosaccharides.

Examples of alpha glucose polysaccharides

Glycogen and Starch

Example of beta glucose polysaccharides

Cellulose

Why is life based on carbon?

- Carbon can readily form 4 bonds with other carbon atoms;

- Carbon forms a backbone for other atoms can be attached

What is the test for reducing sugars?

- Add 2cm^3 Benedict's reagent to 2cm^3 food sample in liquid form

- Place in boiling water bath for 5 mins

- Turns from blue to brick-red

Why is Benedict's test semi quantitative?

The range of colours for a positive result mean that we can estimate the approximate amount of reducing sugar in a sample

What is the test for non-reducing sugars?

- Add 2cm^3 Benedict's reagent to 2cm^3 food sample in liquid form

- Place in boiling water bath for 5 mins

- A negative result shows absence of a reducing sugar

- Add another 2cm^3 food sample to dilute HCl and place in boiling water bath for 5 mins

- Slowly add sodium hydrogencarbonate solution to neutralise the HCl as Benedict's reagent only works in alkaline conditions

- Retest with Benedict's

- If a non reducing sugar was present originally a brick red precipitate should now form

Where is starch found?

Plants - starch grains in chloroplasts and also in seeds

What is the test for starch?

- Place 2cm3 of the sample being tested into a test tube.

- Add two drops of potassium iodide solution and shake.

- The presence of starch is indicated by a blue-black coloration

What are the forms of starch?

amylose and amylopectin

What is amylose?

Amylose = Unbranched polymer (1,4 glycosidic) that forms a helical shape, making it more compact for storage.

What is amylopectin?

Amylopectin = Branched polymer (1,4 and 1,6 glycosidic) of glucose molecules. Branching chains have many terminal glucose molecules that can be broken down rapidly when energy is needed.

What is the function of starch?

energy storage in plants

How is starch adapted to its function?

1) large and insoluble - doesn't diffuse out of cells or affect water potential

2) Compact - lots can be stored in a small space

3) Branched form (amylopectin) - terminal glucose molecules acted on simultaneously by enzymes and quickly broken down

4) Hydrolysed to form alpha glucose- easily transported and used in respiration

Where is glycogen found?

Animals (small granules in muscles and liver) and bacteria

Structural difference between starch and glycogen?

Glycogen has shorter chains and is more highly branched

What is the function of glycogen?

energy storage however fat is the main storage molecule for animals

How is glycogen adapted for its function?

1) Insoluble - no osmotic effect + glycogen does not diffuse out of cell

2) Compact so large amounts can be stored in a small space

3) Many side branches therefore more terminal glucose molecules that can be acted on simultaneously by enzymes and quickly broken down, needed for animals due to high metabolic rate

What is the structure of cellulose?

- Cellulose consists of a long, straight chain (1,4 glycosidic) of β glucose subunits

- These chains run parallel to each other and form cross-linkages via hydrogen bonds

- Forming strong microfibrils, arranged to form fibres

What is the function of cellulose?

Major component in plant cell walls which provides strength and rigidity, preventing bursting via osmosis and maintaining turgid and rigid shape to prevent wilting and maximise SA for photosynthesis

How is cellulose adapted to its function?

1) Forms long, straight and unbranched chains of beta glucose

2) Chains run parallel to each other forming many hydrogen bonds which increase its strength

3) these molecules are grouped to microfibrils and then to fibres, providing more strength

What are characteristics of lipids?

- Contain C,H and 0

- Higher proportion of C-H than carbohydrates

- Insoluble in water

- Soluble in organic solvents

What are tryglycerides?

Lipids formed from the condensation of 1 glycerol molecule and three fatty acids

What is an ester bond?

a bond formed by a condensation reaction between glycerol and a fatty acid

What is a saturated fatty acid?

Fatty acid without carbon-carbon double bonds, often solids at room temperature as straight chains can lie flat.

What is an unsaturated fatty acid?

a fatty acid with at least one double bond between carbon atoms, forming a kink so that chains cannot lie flat, therefore often liquids at room temperature

What are the roles of lipids?

1. source of energy - provide more than twice as much energy as carbohydrates

2. waterproofing - insoluble in water, forms waxy cuticles

3. insulation - slow conductors of heat so help retain body heat and electrical insulators ( forms myelin sheath)

4. protection - stored around delicate organs

Where is an ester bond formed?

between carboxyl group and hydroxyl group

Structure of triglycerides related to their properties

1) triglycerides have a high ratio of energy storing C-H bonds to carbon atoms - excellent source of energy

2) low mass to energy ratio - good storage molecules + lots of energy can be stored in small volume

3) insoluble in water - storage doesn't affect osmosis or water potential in cells

4) high ratio of hydrogen to oxygen atoms, they release water when oxidised - provide source of water eg fat in camel humps

What is a phospholipid?

It is a lipid that has a phosphate group attached to the glycerol and only two fatty acid chains.

Significance of phosphate group in phospholipids

- phosphate group is hydrophilic and attracts water

- fatty acids are hydrophobic and repel water

therefore phospholipids have a polar and non- polar end and will orient themselves so the phosphate head is facing water and the fatty acid tails are facing away ( bilayers and micelles)

The structure of phospholipids related to their properties

1) phospholipids have a polar and non-polar end - in an aqueous environment phospholipids form a bi-layer within cell surface membranes > a hydrophobic barrier is formed between the inside and outside of a cell

2) the hydrophilic phosphate heads help hold at the surface of cell surface membrane

3) the phospholipid structure allows them to form glycolipids by combining with carbohydrates within cell surface membrane for cell recognition

Test for lipids

1. Take a dry and grease free test tube

2. Add 5cm^3 ethanol to 2cm^3 of crushed/grinded sample being tested.

3. Shake tube thouroughly to dissolve lipid.

4. Add 5cm^3 water and gently shake.

5. Milky white emulsion = lipid present

6. Repeat using water instead of sample as a control- should be clear.

Why is an emulsion formed in the emulsion test?

The lipid is finely dispersed in the water so that when light passes through, it is refracted as it passes from oil droplets to water, therefore appearing cloudy

What are amino acids?

the monomers from which combine to form polypeptides which combine to form proteins

What is the general structure of an amino acid?

Central carbon attached to:

1) an amino group (NH2),

2) a carboxyl group (COOH),

3) a hydrogen atom,

4) a variable (R) group

How many amino acids are common in all organisms?

20

What is a peptide bond?

bond formed between two amino acids in a condensation reaction

What is a dipeptide?

2 amino acids joined by a peptide bond

What is a polypeptide?

Long chain of amino acids formed by the condensation of many amino acids

Where is a peptide bond formed?

between the carboxyl group of one amino acid and the amino group of another amino acid

What is the primary structure of a protein?

The sequence of amino acids in the polypeptide chain, held together by peptide bonds, determined by DNA and is responsible for the proteins ultimate shape and function

What is the secondary structure of a protein?

1) Twisting of the alpha helix

2) Beta sheets

these shapes are formed via hydrogen bonds between the slightly negative C=O and the slightly positive N-H

What is the tertiary structure of a protein?

folding of a polypeptide chain further from secondary to form a more complex, specific 3D shape, determined by primary structure.

- disulphide bridges

- ionic bonds

- hydrogen bonds

What is the quaternary structure of a protein?

Larger proteins form complex molecules containing multiple polypeptide chains and prosthetic groups e.g. haem in haemoglobin

Test for proteins

Biuret test - blue Biuret reagent turns purple if protein is present

What are enzymes?

Globular proteins that are biological catalysts that speed up reactions without being used up themselves

How do enzymes speed up chemical reactions?

by lowering the activation energy

What is the structure of an enzyme?

They are globular proteins with a specific 3D shape due to their primary structure, a specific region is functional known as the active site.

What is an enzyme-substrate complex?

physical interaction between enzyme and substrate

What is the induced fit model?

substrate has a complementary shape and enters an enzyme's active site and the enzyme alters its shape slightly so the substrate can fit, as it changes shape it puts a strain on the substrate molecule and distorts particular bonds, lowering the activation energy

Limitations of lock and key model

doesn't indicate how a competitor for an active site can fit into active site even though its not the exact shape as the active site, therefore their cannot be just one 'key' but rather the active site is flexible

What needs to happen for an enzyme to work?

- needs physical contact with its substrate

- have an active site that fits the substrate

Effect of temperature on enzyme activity

-As temperature increases, so does the rate of reaction as particles collide more and form more enzyme-substrate complexes, up until the optimal temperature.

-After the optimal temperature, the rate of reaction decreases because the enzyme's active site changes shape as hydrogen bonds are broken. -Eventually, the enzyme will stop working all together as it is denatured.

Why do we have a slightly lower temperature than optimum for many enzymes?

- although would increase enzyme activity, the advantages would be offset by the energy required to maintain this temperature

- other proteins would denature at higher temperatures

- at higher temperatures any unusual temperature increase e.g. illness might denature the enzymes

Effect of pH on enzyme activity

All enzymes work best at optimal pH. above and below the optimal pH the rate of reaction decreases. Extreme pH changes can denature the enzyme.

- a change in pH alters charges on amino acids in active site, so enzyme-substrate complexes cannot be formed

- extreme changes can break tertiary structure bonds

Effect of enzyme concentration on rate of reaction

As long is there is an excess of substrate, an increase in the amount of enzyme will lead to a proportionate increase in the rate of reaction. If the substrate is limiting, increasing enzyme conc. will have no impact.

Effect of substrate concentration on rate of reaction

If there is a fixed enzyme concentration and the substrate concentration is slowly increased the rate of reaction increases until the substrate concentration is in excess where rate of reaction would level off as the enzymes are saturated

What is an enzyme inhibitor?

Substances that directly or indirectly interfere with the functioning of the active site of an enzyme and so reduce its activity

What are competitive inhibitors?

Molecules that bind to the active site of an enzyme and inhibit the ability of the substrate to bind. This creates a competition between competitive inhibitor and substrate.

An increase in inhibitor conc. reduces rate

An increase in substrate conc. increases rate

What is non-competitive inhibitor?

An inhibitor which works by binding to the enzyme at a site away from the active site (allosteric site) which causes the active site to change shape.

An increase in substrate conc. has no impact.

What does DNA do?

stores hereditary material responsible for passing genetic information from cell to cell and generation to generation

What does RNA do?

transfers genetic information from DNA to ribosome

What are ribosomes made from?

rRNA and proteins

What is the monomer of DNA/RNA?

nucleotides (which means that nucleic acids are composed of multiple nucleotides)

(DNA/RNA are polymers of nucleotides)

Nucleotide structure

- pentose sugar,

- phosphate group,

- nitrogen-containing organic base

Examples of nitrogenous bases?

adenine, guanine, cytosine, thymine, uracil

How are nucleotide components joined?

Condensation Reaction

Product of condensation of 2 mononucleotides

A dinucleotide - bonded via a phosphodiester bond between the deoxyribose sugar and phosphate group

Condensation of many nucleotides

polynucleotide

Structure of RNA

Single, relatively short, polynucleotide chain

- pentose sugar is ribose

- uracil replaces thymine

Structure of DNA

2 extremely long polynucleotide chains joined together via hydrogen bonds between specific complementary base pairs forming a double helix

What are the base pairing rules for DNA?

A-T ~ adenine is complementary to thymine

G-C ~ guanine is complementary to cytosine

How is DNA a stable molecule?

1) phosphodiester backbone protects more chemically reactive organic bases inside the double helix,

2) hydrogen bonds between bases: 2 between A-T and 3 between C-G therefore more C-G = more stable

How is DNA adapted to its function?

1) very stable structure: passes onto generations with minimal mutations

2) double stranded joined only with hydrogen bonds so they can separate during DNA replication and protein synthesis

3) an extremely large molecule > carries immense amount of genetic information

4) base pairs within helical cylinder of backbone means genetic information is protected from being corrupted by chemical and physical forces

5) base pairing leads to DNA being able to replicate and transfer information as mRNA

4 requirements of semi-conservative replication

1) the 4 types of nucleotide each with bases A,T,C,G

2) Both strands of the DNA act as a template for the attachment of these nucleotides

3) the enzyme DNA polymerase

4) a source of chemical energy to drive the process

Process of semi-conservative replication

1) Enzyme DNA helicase breaks hydrogen bonds between bases on the 2 polynucleotide DNA strands, making helix unwind to form 2 single strands.

2) Each exposed polynucleotide strand then acts as a template to which complementary free nucleotides bind by specific base pairs

3) Nucleotides are joined together via a condensation reaction by the enzyme DNA polymerase, forming phosphodiester bonds and 2 identical DNA molecules

4) Each of the DNA molecules contains one of the original DNA strands

Structure of ATP

- adenine,

- ribose,

- 3 phosphate groups

How does ATP store energy?

The bonds between the phosphate groups are unstable and so have a low activation energy. This means they can be easily broken - when they break large amounts of energy is released

- hydrolysis reaction forming ADP and Pi (catalysed by ATP hydrolase)

Synthesis of ATP

conversion of ATP to ADP is reversible therefore can undergo a condensation reaction catalysed by ATP synthase to form ATP from ADP

Where does ATP synthesis occur?

- in chlorophyll containing plant cells during photosynthesis (photophosphorylation)

- in plant and animal cells dying respiration (oxidative phosphorylation)

- in plant and animal cells when phosphate groups are transferred from donor molecules to ADP (substrate-level phosphorylation)

Why is ATP a good energy donor?

it's instability of its phosphate bonds - however this means it's also not a good long term store like fats

- it's therefore the immediate energy source

Why is ATP a better immediate energy source than glucose?

- Each ATP molecule releases less energy than each glucose molecule. The energy for reactions is therefore released in smaller, more manageable quantities

- The hydrolysis of ATP to ADP is a single reaction that releases immediate energy catalysed by ATP hydrolase. The breakdown of glucose is a long series of reactions and therefore the energy release takes longer.

Energy requiring processes that use ATP

- metabolic processes (eg forming starch from glucose)

- movement (energy for muscle contraction)

- active transport (changing shape of carrier proteins)

- secretion (forms lysosomes)

2 ways hydrolysis of ATP is used in cells

1) to provide energy for other reactions

2) to add phosphate to other substances and make them more reactive

Why is water a dipolar molecule?

oxygen atom is slightly negative and hydrogen atoms are slightly positive

What is the significance of water being dipolar?

allows the formation of hydrogen bonds that cause water molecules to stick together and give water it's strange properties