Biology - Chapter 1: Biological Molecules

Monomers

a small repeating molecule / unit that joins other identical molecules to form a polymer.

3 examples of monomers

monosaccharides, amino acids and nucleotides

Polymer

a long chain of repeating molecules, called monomers.

Two examples of polymers

Carbohydrates and proteins

Polymerisation

the process by which monomers join together to form a polymer.

Condensation reaction

a chemical reaction where two smaller molecules react to produce a larger molecule with a covalent bond, resulting in the removal of water.

Hydrolysis reaction

a chemical reaction where the covalent bond in a larger molecule breaks by the addition of water, forming two smaller molecules.

Metabolism

all the chemical reactions that take place in living organisms.

Organic molecule

a molecule that contains carbon (and hydrogen, oxygen or nitrogen)

Monosaccharide

a single sugar - sweet-tasting, soluble.

Disaccharide

two monosaccharides bonded together

Polysaccharide

a long chain of many monosaccharides - insoluble as they are very large molecules

General formula of monosaccharide

(CH2O)n [n = any number from 3 to 7]

Three examples of monosaccharides

glucose, fructose, galactose

Reducing sugar

a sugar (all monosaccharide and some disaccharides) that donates electrons to another chemical, causing the chemical to be reduced

Testing for reducing sugars with Benedict's reagent

1. pour 10cm3 of food sample (measure with pipette) to test tube (if solid, grind in water with pestle and mortar, then filter out remaining solid)
2. pour equal amount of Benedict's reagent
3. heat sample with Benedict's reagent in a water bath of boiling water for 5 mins
4. observe - colour changes depending on amount of sugar present

Why does Benedict's reagent change colour?

initially, solution of blue copper (II) sulfate. adding reducing sugars causes copper (II) sulfate to be reduced, forming solution of orange copper (I) oxide.

Alternate way of comparing amounts of reducing sugars

Carry out Benedict's reagent test, then filter and dry precipitate in each sample and weigh it. heavier sample = more amounts of reducing sugar

When testing for reducing sugars with Benedict's reagent, why is it not possible to distinguish between very concentrated samples, even when concentration is different?

once all copper (II) sulfate is reduced, reducing sugars make no difference to amount of copper (I) oxide (no colour change).

How is maltose formed?

glucose + glucose

How is sucrose formed?

glucose + fructose

How is lactose formed?

glucose + galactose

What reaction takes place when monosaccharides join?

a condensation reaction between two hydroxyl (OH) groups - first glucose molecule loses H, second one loses OH, removed to form water.

What bond forms when monosaccharides join?

a glycosidic bond

How do you break down a disaccharide into its constituent monosaccharides?

hydrolysis - add water

How to test for non-reducing sugars?

BEFORE: test with Benedict's reagent - stays blue and is negative
1. add 2 cm3 of food sample to 2 cm3 of dilute HCl to a test tube.
2. put the test tube in a hot water bath for 5 minutes - BOIL with HCl. (dilute HCl will hydrolyse the disaccharide into monosaccharides.)
3. slowly add sodium hydrogencarbonate solution to test tube (neutralises HCl as Benedict's reagent works in alkaline conditions).
4. test pH with pH paper
5. carry out the test for reducing sugars. - HEAT with Benedict's reagent (reducing sugars should now be present as they were produced from hydrolysis, there should be a colour change from blue -> orange-brown)

Why are polysaccharides suitable for storage?

they are very large molecules so are insoluble.

3 examples of disaccharides

maltose, lactose, sucrose

2 examples of polysaccharides

cellulose and starch

How to test for starch?

1. place 2 cm3 of sample into test tube / add drops into spotting tile depressions
2. add two drops of iodine and shake/stir
3. observe colour change: yellow -> blue-black

Alpha glucose vs beta glucose

- Position of hydrogen and hydroxyl group on first carbon in beta glucose is inverted.
- B is NOT for bottom (both OH on bottom in alpha glucose)

Starch structure and function (5)

- polymer of chains of a-glucose: can be easily hydrolysed to provide respiratory substrate to release energy through respiration
- branched: more ends for faster hydrolysis
- coiled: compact - lots can be stored in a small space
- insoluble: does not affect water potential of the cell
- large and insoluble: cannot diffuse out of the cell

Glycogen structure and function (5)

- polymer of chains of a-glucose: can be easily hydrolysed to provide respiratory substrate to release energy through respiration
- branched: more ends for faster hydrolysis
- coiled: compact - lots can be stored in a small space
- insoluble: does not affect water potential of the cell
- large and insoluble: cannot diffuse out of the cell

Cellulose structure and function (5)

- made of B-glucose, glycosidic bonds between them: forms STRAIGHT unbranched chains, run parallel to each other
- each adjacent B-glucose molecule rotates 180° (alternates): allows hydrogen bonds (cross-links) to form between each chain, making them stronger and rigid (as hydrogen bonds are hard to break), forming microfibrils
- microfibrils are grouped to form fibres: more strength and rigidity
- makes plant cell rigid + stops it bursting when water enters by osmosis (stems and leaves are turgid, max SA for photosynthesis) - resist turgor/osmotic pressure
- resists digestion by enzymes

5 roles of lipids

1. cell membranes
2. source of energy (higher ratio of carbon atoms to carbon-hydrogen bonds than in carbohydrates)
3. insulation
4. waterproofing
5. protection

How do triglycerides form?

They form in a condensation reaction between one molecule of glycerol and 3 fatty acids, producing an ester bond and resulting in the removal of 3 water molecules.

2 types of fatty acids

1. saturated: no carbon-carbon double bonds, max number of hydrogen atoms bonded to each carbon atom
2. unsaturated: has carbon-carbon double bonds. so not max number of hydrogen atoms bonded to each carbon atom

Triglycerides structure and function (4)

1. high ratio of energy-storing carbon-hydrogen bonds to carbon atoms: can release more energy than carbohydrates
2. low mass to energy ratio: can store a lot more energy in a smaller mass (good storage molecules - animals carry less mass for same amount of energy)
3. insoluble: does not affect water potential of the cell and draw water in by osmosis
4. high ratio of hydrogen to oxygen atoms: when hydrolysed, can release water (good for desert organisms)

2 features of phospholipids

1. one of the fatty acids is replaced by a phosphate group (the head) - hydrophilic, orients towarsd water
2. the 2 fatty acids (the tail) - hydrophobic, orients away from water

Phospholipids structure and function (3)

- polar molecules (hydrophilic head, hydrophobic tail): forms bilayer in cell membrane in aqueous environment
- has phosphate group 'head': help to hold at surface of cell-surface membrane
- structure allows them to form glycolipids by combining with carbohydrates: important in cell recognition

4 chemical groups attached to carbon in an amino acid

1. Carboxyl group -COOH
2. Amine group, -NH2
3. Hydrogen atom, -H
4. R group (each amino acid has a different R group)

Name of bond that forms between amino acids

Peptide bond

How does the primary structure of proteins form?

Condensation reaction between amino acids (-OH from carboxylic acid and -H from amine group combine to form water), forms peptide bonds, creates specific sequence of amino acids.

The primary structure of proteins

A sequence of amino acids in a polypeptide chain. The order of amino acids determines the shape and function of the protein.

The secondary structure of proteins

The primary structure (polypeptide chain) is twisted into a 3D shape: an a-helix or B-pleated sheet.

How does the secondary structure of proteins form?

In a condensation reaction, where hydrogen bonds form between the amine group and carboxyl group of a polypeptide chain to make a-helixes or B-pleated sheets (hydrogen of -NH group has overall positive charge, while oxygen of -C=O group has overall negative charge)

Tertiary structure of protein

Secondary structure of protein is twisted and folded into a more complex shape due to disulfide bridges / ionic bonds / hydrogen bonds forming

3 bonds in tertiary structure of protein and their strength

Disulfide bridges - fairly strong, not easily broken
Ionic bonds - weaker than disulfide bridges and are easily broken by changes in pH (form between carboxylic and amino groups not involved in forming peptide bonds)
Hydrogen bonds - easily broken (numerous present)

Quarternary structure of proteins

2 or more polypeptide chains bonded together. May include prosthetic (non-protein) groups.

2 types of quarternary structure of proteins

1. Globular - metabolic functions
2. Fibrous - structural functions (long chains that run parallel to each other, cross bridges between chains)

Test for proteins

1. Prepare liquid sample of food and pour 5 cm3 to a test tube
2. Add an equal volume of Biuret's re-agent to the sample
3. Observe the colour change - if proteins are present, colour change from blue to lilac

Enzymes

Biological catalysts - speed up the rate of the reaction by reducing the activation energy without being used up

Activation energy

The minimum amount of energy needed to start a chemical reaction

What forms when the substrate binds with the enzyme?

Enzyme-substrate complex - substrate is held by temporary bonds that form between certain amino acids in active site and groups on the substrate molecule.

Induced fit model of enzymes (4)

- Substrate binds to enzyme, forms and enzyme-substrate complex
- Active site changes shape slightly to be complementary to substrate
- This distorts/stresses/breaks bonds in the substrate
- Reducing the activation energy

2 things needed in order for an enzyme to work

Must come in physical contact with substrate
Must have an active site that is complementary to the substrate

2 ways to measure rate of reaction

Rate at which reactant is used up (reactant conc falls)
Rate at which products form (final mass falls due to gas escaping / increases due to solids forming)

How does temperature affect rate of reaction?

Increasing temperature:
- increases KE
- molecules move faster, collide with each other more frequently; enzyme and substrate molecules collide more frequently
- more enzyme-substrate complexes form
- RoR increases
- past optimum temperature, active site changes shape, more difficult for substrate to bind
- RoR decreases
- temperature continues to increase, enzyme denatures, enzyme cannot function
- RoR decreases more

How does pH affect rate of reaction?

Changing pH
- change in pH changes charges of amino acids in active site, so may no longer form bonds with substrate (can't form enzyme-substrate complex)
- change in pH leads to bonds maintaining enzyme's tertiary structure to break, so active site changes and substrate can no longer fit inside enzyme
- RoR decreases
- if extreme change in pH, enzyme denatures and cannot function anymore

Formula for pH

pH = -log10 (H+)

What bonds between what groups determines the arrangement of the enzyme's active site?

Hydrogen and ionic bonds between -NH2 and -COOH groups

How does enzyme concentration affect rate of reaction?

Increasing enzyme conc (fixed conc of substrate - enzyme is limiting factor)
- more substrates now acted upon
- RoR increases in proportion to increase in enzyme conc
- RoR increases till at maximum; all substrate being acted upon
- increasing enzyme conc beyond this has no effect (enzyme is in excess so RoR levels off)

How does substrate concentration affect rate of reaction?

Increasing substrate conc (fixed conc of enzymes - substrate is limiting factor)
- more enzyme active sites are used and bind to substrates
- RoR increases in proportion to increase in substrate conc
- RoR increases till at maximum; all enzymes being used
- increasing substrate conc beyond this has no effect (substrate is in excess so RoR levels off)

Enzyme inhibitors

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

2 types of enzyme inhibitors

Competitive - bind to active site
Non-competitive - bind to another position of enzyme NOT active site

Competitive inhibitors (6)

- has similar shape to substrate, can fit in active site
- binds to enzyme's active site instead
- prevents E-S complexes from forming, fewer E-S complexes form
- inhibitor not permanently bound to active site, so when it leaves, another molecule can bind instead
- eventually, all substrate will occupy an active site
- increasing conc of substrate reduces effectiveness of inhibitors
- increasing conc of inhibitors increases time before all substrate occupy an active site

Non-competitive inhibitors (4)

- bind to allosteric site of the enzyme
- alters shape of enzyme and so of active site so substrate can no longer bind to it
- enzyme can no longer function
- does not compete with substrate for active site, so increasing conc of substrate does not decrease effect of inhibitor

Test for lipids (5)

1. Measure 2 cm3 of sample and pour into grease-free test tube.
2. Add 5 cm3 of ethanol
3. Shake the tube.
4. Add 5 cm3 of distilled water
5. Observe the sample - if lipids are present, a cloudy-white emulsion should form

What to put in control tube when investigating the effect of different factors on enzyme activity?

- Same initial concentration of substrate
- Same concentration of DENATURED enzymes
- Same volume of buffer solution

Why might two proteins with the same amino acids have a different tertiary structure?

- Different primary structure / sequence of amino acids
- Hydrogen bonds, ionic bonds and disulphide bridges from between different amino acids

What are a-glucose and B-glucose called?

Isomers of glucose

How do phospholipid molecules form?

Condensation reaction between one molecule of glycerol and 2 fatty acids, which forms an ester bond and results in the removal of water.

2 types of glycosidic bonds

1. 1,4-glycosidic bond (between 1st carbon and 4th carbon)
2. 1,6-glycosidic bond (between 1st carbon and 6th carbon)

What is a fatty acid made up of?

A hydrocarbon chain (R group) and a carboxyl group

Symbol for a fatty acid

RCOOH

In lipid molecules, where does the ester bond form?

Between the hydroxyl group on the glycerol molecule and the carboxyl group on the fatty acid - OH from glycerol and H from fatty acid are removed to make a molecule of water, leaving O from fatty acid.

What is starch hydrolysed into?

Maltose

How does the structure of a protein depend on the amino acids it contains? (5)

1. Structure is dependent on order of amino acids (primary structure)
2. Secondary structure is formed by hydrogen bonds between amino acids (form a-helixes or B-pleated sheets)
3. Tertiary structure formed by hydrogen bonds / ionic bonds / disulfide bridges forming between amino acids so the protein twists into a more complicated shape
4. Tertiary structure forms active sites in enzymes / complementary or specific shapes in antibodies/carrier proteins
5. Quaternary structure is two or more polypeptide chains bonded together (may also have prosthetic groups)

What does the primary structure of a protein determine?

The protein's shape and its function

What types of sugars are reducing sugars?

All monosaccharides and some disaccharides

What type of glycosidic bonds are in glycogen?

1,4-glycosidic bonds and 1,6-glycosidic bonds

What type of glycosidic bonds are in cellulose?

1,4-glycosidic bonds

Triglycerides vs Phospholipids (3+4)

SIMILARITIES:
1. Both contain ester bonds
2. Both contain glycerol
3. Both insoluble in water

Differences:
1. While both contain carbon, hydrogen and oxygen, phospholipids also contain phosphorus
2. Triglycerides 3 fatty acids vs Phospholipids 2 fatty acids
3. Triglyceride hydrophobic vs Phospholipids hydrophilic and hydrophobic region
4. Phospholipids form bilayer in water vs Triglycerides don't

Why might a substrate be complementary to two different enzymes?

Each enzyme is complementary to a different part of the substrate