MODULE 2 SECTION 2 - BIOLOGICAL MOLECULES Flashcards
Functions of water?
- Reactant in many important chemical reactions, like hydrolysis.
- Good solvent. Good reaction medium.
- Water transports substances around plants and animals.
- Helps with temperature control.
- It is a habitat.
Structure of water?
- Polar molecule
- Has slightly positively charge H atoms and slightly negatively charged O atoms.
- Able to form Hydrogen bonds: The slightly negatively charged oxygen atoms attract the slightly postively charged hydrogen atoms of other water molecules.
- Hydrogen bonding gives water some of its many properties.
Properties of water?
- High specific heat capacity.
- High latent heat of evaporation.
- Very cohesive
- Lower density when solid.
- Good solvent.
High specific heat capcity of water means?
- Provides a thermally stable aquatic habitat.
High latent heat of evaporation means?
- When sweat evaporates, it helps to cool the surface of the skin.
- This property means that water helps in temperature control of organisms.
Very cohesive means?
- Helps water to be transported up plant stems in the transpiration stream.
Lower density when solid means?
- Ice floats on top of liquid water.
- Provides an insulating layer for the water underneath so that the organisms living in the water do not freeze.
- Ice provides a habitat for some organisms such as polar bears.
Good solvent means?
- Some substances can dissolve in it.
- Most biological reactions take place in solution, so water is essential for these reactions to occur.
What is a polar molecule?
A molecule with a slightly positively charged side and a slightly negatively charged side.
How does a positively charged ion dissolve in water?
The slightly negatively charged sides of water molecules are attracted towards the positive ion. This results in the ion being surrounded by water molecules.
What are macromolecules?
Macromolecules are complex molecules with a relatively large molecular mass. Includes: - proteins - lipids - some carbohydrates.
Polymers are a group of macromolecules.
What are polymers?
Polymers are large complex molecules composed of long chains of monomers joined together.
What are monomers?
Small, basic molecular units.
Such as monosaccharides and amino acids.
How are polymers formed?
Most biological polymers are formed from their monomers by condensation reactions.
What is the result of a condensation reaction in polymerisation?
A condensation reaction forms a bond between monomers and also releases a water molecule.
How are polymers broken down?
Broken down by hydrolysis reactions.
A hydrolysis reaction breaks the chemical bond between monomers using a water molecule (opposite of a condensation reaction).
What are carbohydrates made from?
- Most are polymers.
- Elements involved are CHO.
- Monomer is monosaccharides.
Single monosaccharides are also called carbohydrates.
Glucose
Glucose is a monosaccharide with 6 carbon atoms. It means that it is a hexose monosaccharide. 2 forms alpha and beta.
left to right OH:
alpha: down up down down
beta: down up down up.
- Glucose is the main energy source in animals and plants.
- It is soluble, so it can be easily transported.
- Its chemical bonds contain a lot of energy.
Ribose
Ribose is a monosaccharide with 5 carbon atoms. It is a pentose monosaccharide.
It is the sugar component of RNA nucleotides.
How are polysaccharides formed?
- Monosaccharides are joined together by glycosidic bonds.
- These bonds are formed in condensation reactions.
How are polysaccharides broken down?
- By hydrolysis reactions.
- The glycosidic bond between monosaccharides is broken down using a water molecule.
What is a disaccharide?
A disaccharide is formed when two monosaccharides join together:
a glucose + a glucose = maltose
a glucose + fructose = sucrose
a/b glucose + galactose = lactose
glucose, fructose, galactose
maltose, sucrose, lactose.
What is a polysaccharide?
A polysaccharide is formed when more than 2 monosaccharides join together.
E.g:
- amylose
- amylopectin
- glycogen
- cellulose.
Starch
- Main energy storage material in plants.
- Insoluble in water; doesn’t cause water to enter cells by osmosis so cells do not swell. This makes it good for storage.
- Composed of amylose and amylopectin.
Amylose:
- a glucose monomer.
- long, unbranched chain of a glucose.
- coiled structure; makes it compact, making it good for storage.
- 1,4 glycosidic bonds.
Amylopectin:
- a glucose monomer.
- long, branched chain of a glucose.
- lots of branches means that glucose can be released quickly.
- 1,4 and 1,6 glycosidic bonds.
Glycogen
- Main energy storage material in animals.
- a glucose monomer.
- long, branched chain of a glucose.
- similar structure to amylopectin, but with many more side branches.
- lots of branches means that glucose can be released quickly.
- compact molecule, so good for storage.
What is the function of glycogen and starch?
- Glycogen acts as the main energy store in animals.
- Starch acts as the main energy store in plants.
Cellulose
- Major component in plant cell walls.
- Strong fibres means cellulose provides structural support for plant cells.
- b glucose monomer.
- long, unbranched chains of b glucose.
- beta glucose molecules join to form straight cellulose chains (each adjacent b glucose molecule is inverted).
- cellulose chains are linked together by hydrogen bonds to form strong fibres called microfibrils.
What are lipids?
- They are macromolecules.
- Elements: CHO
- Triglycerides, phospholipids, cholesterol.
Triglycerides structure
- 1 glycerol molecule, 3 fatty acid molecules attached.
- Made by the formation of an ester bond between each fatty acid and the glycerol molecule.
- Process in which triglycerides are made is called esterification.
Ester bonds
- formed in a condensation reaction, where a water molecule is released.
- broken in a hydrolysis reaction, using a water molecule. (Triglycerides break down when the ester bonds are broken).
Fatty acids
- Fatty acid molecules have long hydrocarbon tails (C and H only).
- Tails are hydrophobic (repel water molecules).
- Causes lipids to be insoluble in water.
Saturated fatty acids:
- no double bonds between C atoms in their hydrocarbon tails.
Unsaturated fatty acids:
- have at least 1 double bonds between C atoms in hydrocarbon tail, causing the chain to kink.
Phospholipids structure
- similar to triglycerides, but one fatty acid molecule is replaced by a phosphate group.
- phosphate head is hydrophillic, fatty acid tails are hydrophobic.
Cholesterol structure
Hydrocarbon ring structure attached to a hydrocarbon tail. Ring has a polar OH group attached to it.
Triglycerides function
- Mainly used as an energy storage molecule in animals and plants.
- some bacteria use triglycerides to store both energy and carbon.
- Good for storage because the long hydrocarbon tails of the fatty acids contain lots of chemical energy (lots of energy is released when broken down).
- lipids contain 2x as much energy per gram as carbohydrates.
- Insoluble, so do not cause water to enter cells by osmosis which would make them swell.
- triglycerides bundle together as insoluble droplets with the hydrophobic fatty acid tails facing inwards and the glycerol heads facing outwards.
Phospholipids function
- Found in cell membranes of all eukaryotes and prokaryotes.
- They make up the phospholipid bilayer.
- Cell membranes control what enters and leaves a cell.
- Hydrophobic fatty acid tails face inwards away from water and hydrophilic phosphate heads face out towards the water on either side, forming a bilayer.
- Centre of bilayer is hydrophobic (fatty acid tails), so water-soluble substances cannot pass through it directly (membrane acts as a barrier to water-soluble substances).
Cholesterol function
- In eukaryotes, cholesterol helps to strengthen the cell surface membrane by interacting with the phospholipid bilayer.
- Cholesterol has a small size and flattened shape. Allows it to fit in between the phospholipid molecules in the membrane.
- Cholesterol molecules bind to the fatty acid tails of the phospholipids, causing them to pack more closely together. Helps to make the membrane less fluid and more rigid.
- Regulates the fluidity of the cell surface membrane.
What are proteins made from?
- Proteins are polymers.
- amino acids are the monomers.
- dipeptide forms when 2 AA join together, polypeptide when more than 2 AA.
- Proteins are made from one or more polypeptides.
Amino acids?
- All AA have the same general structure.
- Carboxyl group (COOH) and amino group (NH2) attached to a carbon atom.
- Variable R group attached to same carbon atom. This is different for every AA.
- Elements are CHONS.
Elements in proteins?
CHONS
How are dipeptides and polypeptides formed?
- AA join together by peptide bonds, formed in a condensation reaction (water molecule is released).
How are dipeptides and polypeptides broken down?
- Peptide bonds between the AA are broken down in a hydrolysis reaction using a water molecule.
Primary structure of a protein?
This is the sequence of amino acids in the polypeptide chain.
Bonds involved:
- peptide bonds.
Secondary structure of a protein?
Alpha helix or Beta pleated sheet.
Bonds involved:
- Hydrogen bonds.
Tertiary structure of a protein?
The final 3D structure of proteins made from a single polypeptide chain.
Bonds involved:
- Hydrogen bonds
- Ionic bonds
- Disulfide bridges
- Hydrophobic and hydrophilic interactions.
Quaternary structure of a protein?
- The final 3D structure of proteins made from more than one polypeptide chain.
Bonds involved:
- Hydrogen bonds
- Ionic bonds
- Disulfide bridges
- Hydrophobic and hydrophilic interactions.
Globular proteins
- round and compact
- soluble, so they are easily transported in fluids.
- they are fairly reactive.
Globular protein example - Haemoglobin
- Globular protein
- Function is to carry oxygen around the body in red blood cells.
- Also a conjugated protein. It means that it is a protein with a prosthetic group (non-protein group) attached.
- Prosthetic group is haem group, which contains iron, which oxygen binds to.
- Haemoglobin consists of 4 subunits - 2 alpha and 2 beta. Each subunit contains a haem prosthetic group.
Globular protein example - Insulin
- Hormone secreted by the pancreas.
- It helps to regulate blood glucose level. (reduces blood glucose levels when they get too high).
- soluble: it can be transported in the blood to the tissues where it acts.
- consists of 2 polypeptide chains linked together by disulfide bonds.
Globular protein example - Amylase
- Enzyme that catalyses the breakdown of starch in digestive system.
- Made from a single polypeptide chain.
- Amylase’s secondary structure consists of both alpha helix and beta pleated sheet sections.
- Most enzymes are globular proteins.
What are the two types of proteins?
Globular proteins:
- Haemoglobin (also a conjugated protein)
- insulin
- amylase (most enzymes are globular proteins).
Fibrous proteins:
- Collagen
- Keratin
- elastin
Fibrous protein example - Collagen
- Found in animal connective tissues such as bone, skin and muscle.
- Very strong/tough molecule with a rope-like structure.
- Minerals can bind to collagen to increase rigidity.
Fibrous protein example - Keratin
- Found in many external structures of animals such as skin, hair, nails, feathers, horns.
- Can be flexible, or hard and tough.
Fibrous protein example - Elastin
- Found in elastic connective tissue such as skin, large blood vessels, some ligaments.
- Elastin is elastic so it allows tissues to return to their original shape after being stretched.
Fibrous proteins
- Tough
- Strong
- Insoluble
- Rope-shaped
- Fairly unreactive (unlike many globular proteins).
Important cations
- Ca2+
- Na+
- K+
- H+
- NH4+
Important anions
- NO3-
- HCO3-
- Cl-
- PO43-
- OH-
What is Cl- a cofactor of?
Cl- is a cofactor of the enzyme amylase
What is Zn2+ a prothetic group of?
Zn2+ is a prosthetic group for carbonic anhydrase
What is a source of coenzymes?
Vitamins are a source of coenzymes.
Name an ion that acts as a buffer in the blood
HCO3- Hydrogencarbonate.
The biuret test
- Test for proteins.
- Add a few drops of sodium hydroxide solution to the test sample.
- Add some copper(II) sulfate solution.
- If protein is present, solution turns purple. If no protein is present, solution remains blue.
The iodine test
- Test for starch
- Add iodine dissolved in potassium iodide solution to test sample.
- If starch present, colour changes to orange-brown to blue-black. If no starch present, colour remains orange-brown.
Emulsion test for lipids
- Test for lipids.
- Add ethanol to test sample and shake test tube.
- Add water to the resulting solution.
- If lipid is present, solution turns milky. If no lipids is present, solution remains clear.
What are reducing sugars?
- Includes all monosaccharides and some disaccharides.
What are non-reducing sugars?
- E.g sucrose
The Benedict’s test for reducing sugars
- Add benedict’s reagent to test sample and heat in a water bath.
- If reducing sugar is present, there is a change from blue solution to brick-red precipitate.
The Benedict’s test
- If reducing sugars test is negative, non-reducing sugars may be present.
- Add Hydrochloric acid to a new sample of test solution and heat in a water bath.
- the purpose of the hydrochloric acid is to break the reducing sugars down into monosaccharides.
- After, neutralise the solution with sodium hydrogencarbonate.
- Then carry out the bendict’s test like before.
- Add benedict’s reagent to test solution and heat in a water bath.
- If solution remains blue, no non-reducing or reducing sugar present.
- If solution turns from blue solution to brick-red precipitate, non-reducing sugar is present.
Test strips for glucose
Glucose can also be tested using glucose test strips.
- The strips are dipped in a test solution, and change colour if glucose is present.
- The colour change can be compared to a colour chart to indicate the concentration of glucose present.
- These strips are useful for testing urine for presence of glucose, which may indicate that the person has diabetes.
Qualitative testing
You use qualitative testing to determine whether a substance is present in a sample or not.
Quantitative testing
Quantitative testing tells you the concentration of a substance present in a sample.
- colorimetry
- biosensors
Colorimetry and benedict’s reagent
You can use Benedict’s reagent and a colorimeter to get a quantitative estimate of the concentration of glucose in a solution.
- A colorimeter is a device that measures strength of a coloured solution by seeing how much light passes through it.
- It measures absorbance.
- The more concentrated the colour of the solution, the higher the absorbance is.
How to find the glucose concentration of an unknown solution?
- Make up several solutions of known glucose concentrations (using serial dilution technique).
- Measure the absorbance of each of these solutions.
- Plot a graph of absorbance against glucose concentration to make a calibration curve.
- The curve can be used to estimate the concentration of the unknown solution.
- It is the easiest to measure the concentration of the blue Benedict’s solution that is left after the test.
- The more glucose present, the paler the solution since more glucose reacted with the benedict’s solution to form the brick red precipitate which is removed.
- Therefore, the higher the glucose concentration, the lower the absorbance of the solution.
Biosensors
A biosensor is a device that uses a biological molecule, such as an enzyme, to detect a chemical.
- The bio molecule produces a chemical signal, which is converted to an electrical signal by a transducer.
- the electrical signal is then processed and used to work out other information.
What is chromatography used for?
It is used to separate substances in a mixture. After separation, you can often identify the components.
Can often be used to separate out and identify:
- amino acids
- carbohydrates
- vitamins
- nucleic acids.
- paper chromatography
- thin layer chromatography.
How do you calculate Rf values?
Rf = distance moved by solute / distance moved by solvent.
How can you use Rf values to identify substances?
You can identify the substances in the mixture by comparing the calculated Rf values with known Rf values of the solutes in a database, or table of known values.
