Biology A-Level - Chapter 3 + 4: Biological Molecules + Enzymes

Monosaccharide

simple sugar molecule

Disaccharide

double sugar molecule made up of two monosaccharides

Polysaccharide

polymer of many simple sugar molecules

Examples of monosaccharides

Glucose, fructose, galactose, ribose, deoxyribose

Examples of disaccharides

sucrose, lactose, maltose

Examples of polysaccharides

starch, amylopectin, amylose, chitin, glycogen

isomers

molecules with the same chemical formula but different molecular structure

Forming maltose

condensation reaction of two alpha glucose

Forming lactose

condensation reaction of glucose and galactose

Forming sucrose

condensation reaction of glucose and fructose

Formula of glucose

C6H12O6

Difference between alpha and beta glucose

on C-1, alpha glucose has a OH group on the bottom and beta glucose has a OH group on the top

Hexose sugar

A sugar with six carbon atoms

Properties and features of glucose

• hexose molecule

• main function = energy source, used in respiration, released energy for production of ATP

• soluble in water as it is polar

• isomer: exists as alpha and beta glucose

condensation reaction

a chemical reaction in which the -OH group of a simple sugar bonds to the -H group of another simple sugar, forming a complex sugar molecule bonded together with a glycosidic bond and water

hydrolysis reaction

where water is used to break down a complex sugar into simple sugars by breaking down the glycosidic bond

Features and properties of amylose

• alpha glucose polymer (forms alpha helix which has hydrogen bonds)

• has 1,4 glycosidic bonds

• unbranched and compact

• can be tested for with iodine in a potassium iodide solution

• used for storing energy in plants (starch)

Testing for starch

iodine in a potassium iodide solution: turns from orange to blue-black. works for alpha helix starch molecules as the molecules of potassium iodide fit into the gaps in the helix and reflect a different wavelength of light

Features and properties of amylopectin

• alpha glucose polymer (alpha helix)

• 1,4 AND 1,6 glycosidic bonds

• branched polymer, longer branches, compact

• can be tested for with iodine in a potassium iodide solution

• used for storing energy in plants

Features and properties of glycogen

• alpha glucose polymer

• 1,4 AND 1,6 glycosidic bonds

• branched and compact (shorter branches = more ends = more alpha glucose released more quickly for mammals' high metabolic rate)

• stored in the liver and muscle in mammals as energy store

Features and properties of Cellulose

• beta glucose polymer

• 1,4 glycosidic bonds

• unbranched; chains of beta glucose from microfibrils

• microfibrils joined together with hydrogen bonds; strong and flexible

• used for building up plant cell wall and maintaining rigidity

Pentose sugar

5 carbon sugar

Structure of ribose

5 membered ring with both -OH on bottom on C2 and C3 and -OH on top on C1

Quantitative Benedict's test

1. Use serial dilution of 1% glucose solution to produce 5cm of different concentrations of glucose as well as distilled water and the unknown glucose solution

2. Add 10cm of quantitative Benedict's reagent to each tube and incubate in water bath for 10min

3. Filter each sample into a cuvette using a pipette and funnel and repeat for each sample

4. Rinse the funnel each time to shake off excess precipitate

5. Set colorimeter to red light and transmission and calibrate with distilled water (100%)

6. Measure transmitted light and plot into a calibration curve and interpolate to find unknown solution

Explain why the transmission of red light increases as the glucose concentration in the sample rises

As the glucose concentration increases there are less unreacted molecules of Benedict's reagent so the solution is a paler blue colour; less of the red light wavelength is absorbed meaning the transmission of the red light increases

Why is it necessary to centrifuge the sample before taking the colorimeter reading?

To separate the precipitate and the solution as the precipitate in the solution would make it opaque to all wavelengths of viable light, resulting in inaccurate colorimeter readings

What could we do to obtain an accurate value for concentrations of glucose higher than 1%?

Repeat the experiment and include solutions of glucose with a concentration of above 1% so we can interpolate

Lipids

biological molecules which are only soluble in organic solvents such as alcohols

Use of lipids in the body

storage molecules, buoyancy, waterproofing, insulation, protection

Tryglyceride

3 fatty acids bonded to a glycerol molecule with an ester bond in a condensation reaction, releasing 3 water molecules (when ester bonds are broken, water is released, lowering the pH)

Short-chain fatty acids

hydrocarbon tails with less than 6 carbons

Medium-chain fatty acids

6-10 carbons

Long-chain fatty acids

13-21 carbons

Very long-chain fatty acids

22 or more carbons

Saturated lipids

no carbon double bond, melt at higher temperatures, found in animal fats

Unsaturated lipids

carbon double bond, melt at lower temperatures, found in plants and form oils (C=C bond changes bond direction so the molecule isn't a straight line and can slide over each other, forming oils)

Phospholipids

Two fatty acids bonded to a glycerol molecules via ester bonds as well as a phosphate group

Properties and use of phospholipids

• phosphate heads are hydrophilic (polar)

• fatty acid tails are hydrophobic

• this makes phospholipids ampiphatic

• one fatty acid is saturated and one fatty acid is unsaturated

• form the plasma membrane where the phosphate heads are on the outside and the fatty acid tails on the inside (hydrophobic region = waterproof)

Proteins

Chains of amino acids

Amino acids

monomers of proteins

Structure of amino acid

central carbon, carboxyl group to the right (COOH), amine group to the left (NH2), hydrogen above and R group below

Dipeptide

Two amino acids bonded together with a peptide bond in a condensation reaction, with a byproduct of water

R group

a functional group that defines a particular amino acid and gives it special properties (either acid/basic/polar/non-polar)

Central Dogma of Biology

DNA - Pre-mRNA - mRNA - specific sequence of amino acids - specific shape of protein

Different shapes of protein

globular, conjugate, fibrous

Primary structure of protein

specific sequence of amino acids joined by peptide bonds formed by condensation reactions

Secondary structure of protein

shape of the chain of amino acids determined by the hydrogen bonding - alpha helix or beta pleated sheet

Tertiary structure of protein

• folding and twisting of the alpha helix/beta pleated sheet into a specific 3D shape

• involves four types of bonds (between R groups depending on the chemical nature of R group)

Bonds involved in tertiary structure of protein

ionic bonds, hydrophobic bonds, disulfide bridges, hydrogen bonds

Description of ionic bonds in protein structure

between the negatively charged acidic R groups and positively charged basic R groups

Description of disulfide bridges in protein structure

strong covalent bonds between sulfur atoms of the amino acid cystein

Description of hydrophobic bonds in protein structure

bonds between R groups of non-polar amino acids

Description of hydrogen bonds in protein structure

formed between polar R groups; broken by high temperature and pH

quaternary structure of a protein

results when a protein consists of multiple polypeptide chains

Types of protein

fibrous, globular, conjugated

Structure of globular proteins

• aspherical shape covered by tightly folded polypeptide chains

• chains fold so that non-polar groups are on the inside and polar groups on the outside, so they are usually soluble

Use of globular proteins

• transport proteins

• enzymes

• hormones

Structure of fibrous proteins

• formed from parallel polypeptide chains held together by cross links

• form long, rope-like fibres with high tensile strength

• insoluble in water due to high proportion of hydrophobic R groups in repetitive amino acid sequence

• unaffected by temperature and pH and mainly structural

Structure of conjugated proteins

• globular proteins that contain a non-protein group called a prosthetic group

Structure and properties of haemoglobin

• responsible for binding to oxygen in RBCs

• has 4 polypeptide chains (two alpha, two beta)

• each chain has a "haem" group containing iron (oxygen binding site)

• each binding site can bind to one molecule of oxygen reversibly

• polypeptide chains interacts so that when oxygen binds to one chain, it increases the efficiency of oxygen binding to the others

• positive cooperativity is where haemoglobin changes its shape depending on how much oxygen there is

Structure and properties of catalase

• quaternary protein with 4 haem groups - Fe2+

• different sequence of amino acids to haemoglobin = different bonding = different protein shape

• breaks down hydrogen peroxide into water and oxygen

Structure and properties of collagen

• gives bones "bendability"

• hydrogen bonds form between polypeptide chains

• made up of 3 polypeptide chains of 1000 amino acids, each of which twist around each other

• molecules are insoluble and link up to form fibrils several mm long

Structure and properties of elastin

• elastic fibres found in blood vessel walls and alveoli

• stretch and recoil NOT contract and relax

• made of a polypeptide called tropoelastin

Structure and properties of keratin

• found in hair, skin, nails

• large proportion of cyestine (lots of disulfide bridges)

• strong, inflexible, insoluble

• hair contains fewer bonds, so it is more flexible than nails

Biuret test for proteins

1. Add biuret’s reagant

2. Colour change from blue to purple

Iodine test for starch

1. Add iodine in a potassium iodide solution

2. Colour change from yellow to blue/black

Benedict's test for reducing sugars

1. Add Benedict's reagent and heat in a water bath

2. Sample goes from blue to brick red

Emulsion test for lipids

1. Add ethanol and shake

2. Cloudy precipitate formed

Benedict's test for non-reducing sugars

1. Add dilute HCl.

2. Put in a water bath brought to a boil.

3. Neutralise with sodium hydrogen carbonate

4. Do Benedict's Test for reducing sugars

5. Sample goes from blue to brick red

Examples of reducing sugars

glucose, galactose, fructose, lactose, maltose

Examples of non-reducing sugars

sucrose

Properties of water: Solvent

due to water molecules being polar, they can easily bond to other polar molecules through hydrogen bonds

Properties of Water: Density

ice is less dense than water due to air being trapped inside; ice acts as an insulating layer for aquatic animals and as a habitat

Properties of Water: Transport

water is a liquid at room temperature so is an excellent transport medium as substances can dissolve in water e.g. hormones, glucose, mineral ions

Properties of Water: Metabolite

water is a metabolite in chemical reactions e.g. hydrolysis as it is a polar molecule and an excellent solvent

Properties of water: high specific heat capacity

has a high heat specific capacity so lot of energy required to warm water up; minimising temperature fluctuations in living things

Properties of water: latent heat of vaporisation

high latent heat of vaporisation allows for greater cooling effect for minimal water loss

Properties of water: Freezing capabilities

large bodies of water do not completely freeze over so nutrient current continue so animals can survive

Properties of water: Transparency

water is relatively transparent so light can get through to the seabed for plants to photosynthesise

Properties of Water: Cohesion

water molecules form hydrogen bonds to each other - strong cohesion between molecules enables effective transport of water in tube-like transport cells

Properties of Water: Adhesion

water molecules bind to surfaces e.g. in the xylem

Properties of Water: Tension

water molecules move with each other

Induced fit hypothesis

the active sit can slightly change shape to fit the substrate properly

Number of amino acids in an active site

number of amino acids in active site is very small so there are a small/specific number bonds between active site and substrate, so amino acid is specific

Biological catalyst

a substance that reduces the activation energy of biological reactions without being used up

Anabolism

building up molecules

Catabolism

breaking down molecules

Examples of extracellular enzymes

amylase, lipase, maltase, lactase, trypsin, pepsin

Examples of intracellular enzymes

catalase, DNA polymerase, ATP synthase

Properties and features of catalase

• is a globular and conjugated protein

• catalyses the breakdown of hydrogen peroxide produced as a byproduct of metabolism

• has 4 haem groups

• protects cells from oxidative damage

Properties and features of amylase

• globular simple protein

• catalyses the breakdown of starch into simple sugars

• digestive enzyme

• can be found in the salivary glands and pancreas

• has both alpha helices and beta pleated sheets

Properties and features of trypsin

• digestive enzymes

• breaks down proteins in the small intestine into amino acids

• has a single polypeptide chain

• globular simple protein

• contains disulfide bridges

Properties and features of pepsin

• digestive enzymes

• breaks down proteins in the stomach into amino acids

• globular protein

• has an optimum pH of 2 due to the acidic conditions of the stomach

Description of temperature graph for enzyme activity

• increases with temperature due to increased kinetic energy of enzymes

• peaks at around 37C due to optimum temperature

• increasing beyond optimum temperature denatures enzyme as tertiary bonds break down

Description of pH graph for enzyme activity

• same shape as temperature graph

• reducing/increasing pH away from optimum pH reduces ROR as concentration H+ ions affects the tertiary structure of enzyme molecule as it interferes with R group bonds so 3D shape changes

Description of substrate conc graph for enzyme activity

• increases then plateaus

• increase substrate concentration leads to increased ROR as rate of successful collisions increases so more ESCs formed

• plateaus after as all enzymes present are working at maximum rate so enzyme rate stays the same - Vmax

Description of enzyme concentration graph for enzyme activity

• increases then plateaus

• increase enzyme concentration leads to increased ROR as rate of successful collisions increases so more ESCs formed

• plateaus after as there is a fixed concentration of substrate so no more can be broken down so ROR stays the same - Vmax

Temperature coefficient for enzymes (Q10)

measure of how much ROR increases for every 10C increases - most enzyme reactions have a Q10 of 2 so enzyme activity doubles with an increase of 10C

Effect of H+ ions on enzymes

Hydrogen bonds join oppositely charged R groups together; as H+ increase, they take the place of hydrogen bonds, denaturing the enzyme

Enzyme inhibitors

molecules with a similar shape to the active site and slow or prevent an ESC from forming