New 2.2 - Biolgical Molecules Flashcards
How maltose made?
2 alpha glucose molecules
How sucrose is made
Alpha-glucose and fructose
How lactose is made
Beta-galactose and alpha-glucose
How is cellulose made
Two beta-glucose molecules
How are disaccharides formed and broken?
Formed - by condensation reaction
Broken - by hydrolysis reaction
Structure of amylose
Long unbranched chain of alpha-glucose molecules. Has glycosidic bonds on carbons 1,4.
It coils into a spiral shape via hydrogen bonds
Structure of amylopectin
Branched chain of alpha-glucose molecules with glycosidic bonds on carbons 1,4 and 1,6.
Coils into a spiral shape, with hydrogen bonds.
Structure of glycogen
Long chain of branched alpha-glucose molecules
Contains glycosidic bonds on carbons 1,4 and 1,6.
1,4 bonded chains are smaller than amylopectin, so doesn’t coil.
More branches makes it more compact, easier to remove monomer units.
How would many glucose molecules dissolving in cytoplasm affect water potential of the cell?
- more negative water potential
- Water moves into the the cell, via a partially permeable membrane, as solute concentration in the cytoplasm increases.
Structure of cellulose - mechanism
Straight, unbranched chains of beta-glucose molecules with glycosidic bonds on carbons 1,4
Hydrogen and hydroxyl groups on beta glucose are inverted, so the chain is rotated every other beta-glucose molecule by 180 Degrees, stops the chain spiralling.
-Contains hydrogen bonding between beta-glucose molecules which gives it strength and stops the chain spiralling
Why are polysaccharides good energy stores?
They are insoluble in water
Polysaccharides hold glucose molecules in chains, so they can be easily ‘snipped off’ when required for respiration.
Glycogen and starch are compact, so occupy less space as dense granules within the cell.
Some are branched - more compact, and glucose molecules can be snipped off easier by hydrolysis when energy is required quickly.
Equation for aerobic respiration
Glucose + Oxygen ——> Water + Carbon Dioxide
How do cellulose cell walls form(microfibrils)?
When many cellulose chains are bound together without spiralling, they form microfibrils(10-30nm in diameter)
These microfibrils bundle together to form microfibrils
These are embedded in pectins to form plant cell walls.
Macrofibrils run in all directions criss-crossing the wall for extra strength
Why are plant cell walls strong?
Microfibrils and macrofibrils have high tensile strength - due to glycosidic bonds and hydrogen bonds between chains.
Macrofibrils run in all directions, criss-crossing the wall for extra strength
Cellulose is difficult to digest - glycosidic bonds between glucose molecules less easy to break
Function of plant cell wall
Plants do not have a rigid skeleton - each cell needs to have strength to support the whole plant
There is space between macrofibrils for water and mineral ions to pass into and out of the cell - makes the cell wall fully permeable.
Cell wall has a high tensile strength - prevents cells from bursting when turgid - supports plant and protects cell membrane
Macrofibril structure can be reinforced with other substances - for extra support or to waterproof the walls.
Cell walls of other organisms
Bacteria - cell wall made of peptidocglycan
Insects/crustaceans/fungi - cell wall made of chitin
Macromolecule def
A very large, organic molecule
It is not a polymer, as does not have the same repeating units.
Structure of glycerol
Has three carbon atoms
Three free -OH groups
Fatty acid information
Carboxyl group on one end(-COOH)attached to hydrocarbon tail.
Carboxyl group ionises into an H+ and COO- group. This structure is therefore an acid as it can produce free H+ ions.
Different bonds for different molecules
Carbohydrates/polysaccharides - glycosidic bonds
Lipids - ester bonds
Proteins - peptide bonds
If fatty acid is saturated
No Carbon-Carbon double bonds
If fatty acid is unsaturated(effects)
Structure: Fatty acid acid contains C-C double bonds
- Mono/polyunsaturated depending on how many C-C double bonds
Effects: change shape shape of the hydrocarbon chain - gives it a kink
- these kinks push the molecule apart slightly, making molecule more fluid
Formation of triglycerides
Three fatty acid bonded by condensation reaction to the three free -OH groups on a glycerol molecule by ester bonds
Three water molecules are produced
Function of triglycerides
Energy source Energy store Insulation Buoyancy Protection
Structure and formation of phospholipids
- Same structure as triglycerides, except on of the fatty acid groups is replaced with a phosphate group.
- two fatty acids and one phosphate group bind to the three free -OH groups on a glycerol molecule by condensation reaction.
- one of the three -Oh groups in glycerol forms an ester bond
How do phospholipids behave in water and why?
- phosphate group has a negative charge, so it is polar.
- Fatty acid tails are non-polar, so are repelled by water.
- phosphate ‘head’ is hydrophilic, so points to the outwards of the bilayer
- Fatty acid tail is hydrophobic, so points inwards the bilayer
Word describing structure of a phospholipid
Amphipathic
The molecule contains hydrophilic and hydrophobic parts
Description of phospholipid bilayer
- Phospholipids form a bilayer surrounded by aqueous solution
- Tails point inwards, and heads point outwards into the solution
- The individual phospholipids are free to move around in the layer, but won’t move into any position where the hydrophobic tails are exposed to water - gives membrane some stability
- membrane is selectively permeable. Allows membrane to control what goes in and out of the cell, so it can function properly
- only small and non polar molecules can move through the tails in the bilayer.
Structure of cholesterol
H
Function of cholesterol
-Regulates fluidity of the membrane, prevents it from become too fluid or stiff
Where is cholesterol made
Made in the liver in animals
Examples of cholesterol substances
- Can form steroid hormones, testosterone, oestrogen and Vitamin D
- All are small and hydrophobic, so can pass through hydrophobic part of the cell membrane and any other membrane inside the cell
What is a protein?
Large polymers comprised of long chains of amino acids.
Functions of proteins
- Enzymes
- Channel and carrier proteins in membranes that carry substances across by facilitated diffusion and active transport
- They form structural components of animals, e.g. muscles
How many amino acids are there?
20
What are essential amino acids?
The 10 amino acids that can’t be produced in the human body - they need to be consumed or incorporated into the diet.
Structure of amino acids
Contain C,N,H,O
- A carboxyl group
- An amine group
- An R group - a side chain specific to the amino acid, e.g, cysteine has Sulphur in its side chain
Long chain of amino acids
Two amino acids joined
Polypeptide
Two amino acids joined is called a dipeptide
Primary Protein Structure def
The sequence, type and number of amino acids in a polypeptide chain
Secondary Structure def
When sections of polypeptides coil into different shapes:
Alpha-helix
Beta-pleated sheets
Tertiary Structure def
Tertiary structure is further folding of the polypeptide driven by hydrophobic and hydrophilic interactions
Within the final tertiary structure adjacent amino acids may form bonds which stabilise the structure
Bonds included:
- Hydrogen bonds
- Disulphide Bridges
- Ionic bonds
- Hydrogen bonds
Quaternary Structure def
Separate twisted or folded polypeptide subunits linked together
Prosthetic groups may be attached to the quaternary structure of a protein, e.g haem group into haemoglobin.
Or:
The quaternary structure of a protein is the association of several protein chains or subunits into a closely packed arrangement. Each of the subunits has its own primary, secondary, and tertiary structure.
Two shapes in secondary structure
Alpha-helix
Beta-pleated sheets
Types of bonding in proteins
Ionic bonds
Disulphide bonds/Bridges
Hydrogen Bonds
Hydrophobic and hydrophilic interactions
Bond in primary structure
Peptide bonds
Bonds in secondary structure
Hydrogen bonds
Bonds in tertiary strucuture
Ionic bonds
Disulfide Bridges/bonds(only for cysteine)
Hydrophilic and hydrophobic interactions between R groups
Bonds in quaternary structure
Hydrogen bonds
Covalent bonds
2 Different protein structures - info about them
- Fibrous- a relatively long, thin structure, is insoluble in water and metabolically inactive, often having a structural role within an organism.
- Globular - has molecules of a relatively spherical shape, which are soluble in water, and often have metabolic roles within the organism.
What is the 3D structure and shape of a protein, e.g. globular and fibrous proteins.
Tertiary and Quaternary structure
Fibrous proteins info
- Usually made of long polypeptide chains that form fibres
- Insoluble because they have amino acids with hydrophobic R groups
- very strong, but flexible
Globular proteins info
- They roll into a spherical shape
- They are water soluble because they have R groups on the inside that are hydrophobic, and R groups on the outside that are hydrophilic
- Involved in metabolic processes
Prosthetic group def
a non-protein component that forms a permanent part of a functioning protein molecule.
Three Globular proteins
Haemoglobin
Insulin
Pepsin
Three Fibrous Proteins
Collagen
Keratin
Elastin
Collagen info:
- What tissues in the body contain collagen?
It provides mechanical strength:
- in artery walls, layer of collagen prevents artery bursting when withstanding high pressures being pumped from the heart
- Tendons are made of collagen and connect muscles to bones, allowing them to pull on bones
- Bones are made from collagen, and then reinforced with calcium phosphate, which makes them hard
- Cartilage and connective tissue are made from collagen
Keratin info
- Rich in cysteine, so many disulfide Bridges form between its polypeptide chains.
- alongside hydrogen bonding this makes the molecule very strong.
- found in nails, hair, claws etc
- provides mechanical protection
- also provides an impermeable barrier to infection, and as it is waterproof, prevents entry of water-borne pollutants
Elastin info
- strong and extensible due to cross-linking and coiling
- found in skin, which can stretch and return to normal state(e.g. when pinched)
- elastin in lungs allows them to inflate and deflate
- in bladder it expands to hold urine
- helps blood vessels stretch and recoil as blood is pumped through them.
Haemoglobin info
- Quaternary Structure: four polypeptides, two alpha globin chains, two beta-globin chains.
- Contains 4 prosthetic groups attached called a haem group, an Fe2+ group.
- Therefore haemoglobin is a conjugated protein.
- Function: carries oxygen from lungs to the tissues. Oxygen binds to iron in each of the four haem groups.
Insulin info (insulin is a globular protein)
-Made of two polypeptide chains:
A chain begins with a section of alpha helix,
B chain ends with a section of beta-pleat
-Both chains fold into a tertiary structure and are joined by disulfide links/bonds.
- is soluble in water due to amino acids with hydrophilic R groups on the outside
-helps control blood-glucose levels
Pepsin information
- an enzyme that digests protein in the stomach, can survive in high pH conditions
- made up of a single polypeptide chain of 327 amino acids
- folds into a symmetrical tertiary structure.
- contains many amino acids with acidic R groups, explains why it can thrive in high pH environments
Ab initio protein modelling
- a model is built based on the physical and electrical properties of the atoms in each amino acid in the sequence. With this technique, there can be multiple solutions to the same amino acid sequence, and other methods sometimes need applying to reduce the number of solutions.
Comparative protein modelling
- protein threading, which scans the amino acid sequence against a database of solved structures and produces a set of possible models which would match that sequence.
Different inorganic ions
Calcium Sodium Potassium Hydrogen Ammonium Nitrate Hydrogencarbonate Chloride Phosphate Hydroxide
Function of each inorganic ion
- Calcium - transmission of nervous impulses
Regulation of protein channels
Muscle contraction
Hardening teeth and bones - Sodium - involved in transmission of nervous impulses
Active transport Na+ pump
Co-transport of glucose and amino acids across membranes
-Potassium - involved in transmission of nervous impulses, active transport and plant cell turgidity
-Hydrogen - the higher then concentration, the lower the pH of bodily fluids
-Ammonium - source of nitrogen used to make organic molecules
-Nitrate - source of nitrogen for organic molecules
-Hydrogencarbonate - involved in the regulation of blood pH and transport of carbon dioxide in the blood - Chloride - involved in transport of carbon dioxide in the blood through the chloride shift
- Phosphate - components of biological molecules such as nucleotides, ATP, and the formation of the phospholipid bilayer
- Hydroxide - the higher the concentration, the higher the pH of bodily fluids.
Different food tests
-Biuret test - proteins
-Benedict’s reagent- reducing and non reducing sugars
Iodine - starch
Emulsion test - lipids
Describe the test for proteins
Positive results?
Biuret test is added to the sample in solution.
Leave for 5 minutes and observe for a colour change
Positive result is purple
-Usually uses a control of distilled water and a sample with egg albumen
Test for reducing sugars
Positive result?
- Benedict’s reagent is heated to 80Degrees Celsius with a solution of the sample
- Reagent test strips can be used for semi-quantitative results
- On heating, if a reducing sugar is present, there will be a red or orange precipitate
- Intensity of colour depends on concentration of reducing sugars. If there is little it will be green, if there is a high conc. if will turn intense red.
- Use colorimetry and a calibration curve to quantify reducing sugars in a sample
Test for non-reducing sugars
Positive result?
- If a reducing sugar is not present, heat with HCl to reduce the non-reducing sugar.
- Sodium hydrogencarbonate solution is added to neutralise the acid.
- Then the Benefict’s reagent is added before heating to 80 Degrees Celsius
- On heating, if a non-reducing sugar is present, there will be a red or orange precipitate
Test for starch
Positive result?
- Iodine(iodine solution is dripped on to a sample(solid or liquid)
- positive test turns solution from yellow to blue/black
Test for lipids
Positive result?
- Take a sample and mix it thoroughly with ethanol
- Filter the solution
- Pour solution into water
- shake the sample
- if a milky white emulsion is produced, lipids are present.
How do biosensors work?
They take a biological or chemical variable which cannot be easily measured, and convert it into an electrical signal.
Uses of biosensors
- Detect contaminants in water
- Detect pathogens and toxins in food
- Detect airborne bacteria
- Use in bio-terrorism programmes
Principle of chromatography
To separate a mixture into its constituents, in this case the biological molecules.
Stationary phase in chromatography
This is either:
- Strip or piece of paper placed in the solvent
- the thin layer chromatography plate(TLC plate), often a sheet of plastic coated with a thin layer silica gel or Aliminium Hydroxide
- the chromatography paper, made of cellulose
- in each case, there are free -OH groups pointing outwards, in contact with the mobile phase.
What is the mobile phase?
- This is the solvent for the biological molecules
- water used for polar molecules
- ethanol used for non-polar molecules.
- Mobile phase flows through and across the stationary phase, carrying the biological molecules with it.
How to calculate Rf value
- Rf = X/Y
- X =Distance from pencil line to centre of a spot of pigment
- Y = distance from pencil line to solvent front.
Different methods of detecting colourless molecules in chromatography
-UV light —> TLC plates have a chemical which fluorescent under UV light. In UV light, most of the plate will glow, except from the places the spots have travelled to. They mask the plate from UV light.
-Ninhydrin —> To see amino acids, allow the plate to dry and then spray with ninhydrin.
This binds to the amino acids which are then visible as brown or purple spots.
-Iodine —> Allow the plate to dry, and place in enclosed container with a few iodine crystals.
Iodine forms a gas, which binds to the molecules in each of the spots.
How does chromatography work?
H
Uses of chromatography
TLC is used to:
- monitor progress of a reaction, as it works relatively quickly
- urine testing of athletes for illegal drugs
- analysis of drugs for purity of components
- analysis of food to determine the presence of contaminants
Features of primary structure - exam Q
- sequence of amino acids in a polypeptide chain
- peptide bonds
Features found only in secondary structure - exam Q
- Hydrogen bonds
- initial folding of the polypeptide chain
Features found only in the tertiary structure - Exam Q
- the overall 3D shape
- ionic bonds
Features found only in quaternary structure - Exam Q
- alpha and beta subunits
Exam Q - 2 marks
Hydrogen bonds allow water to act as a solvent.
Why is the ability of water to act as a solvent important for the survival of organisms?
- medium for metabolic reactions - it allows ionic compounds and minerals to separate by hydrolysis reaction
- allows substances such as minerals and nutrients to dissolve and be transported in the blood
- able to dilute toxic substances
Describe three other ways in which the structure of haemoglobin differs from that of collagen.
(3 Marks)
- Haemoglobin is a globular protein
- -
Why is glycogen a good storage molecule?
- HhhHhhh
List examples of where hydrogen bonds are found in biological molecules
° Between chains of cellulose ° Between DNA base strands • Protein 3° structure • Protein 2° structure -alpha helices /beta-pleated sheets • AVP;
Cholesterol is transported in the blood within molecules of low-density lipoprotein (LDL). Name two molecules that combine with cholesterol to form LDLs.
(2 Marks)
- Saturated lipids/fats/triglycerides
- proteins/polypeptides
LDL and a similar molecule, high-density lipoprotein (HDL), carry cholesterol in the blood. LDL and HDL affect the formation of atheromas in the arteries.
Describe the different ways in which LDLs and HDLs affect the formation of atheromas
(7 Marks)
LDL:
(carry cholesterol) from liver to, tissues / cells ;
receptors on (tissue) cells ;
raise / AW, blood cholesterol ;
increase / cause, deposition of, fats / lipids / triglycerides / cholesterol, in artery wall / under endothelium ;
under epithelium
form, plaques / atheromas ;
HDL:
(carry cholesterol) from, tissues / body / blood, to liver ;
ACCEPT back to liver
receptors on, hepatocytes / liver cells ;
lower / reduce / decrease, (blood) cholesterol ;
reduce deposition, of fats / lipids / triglycerides / cholesterol ; decrease, formation / risk, of, plaques / atheromas ;
The cells of living organisms require glucose.
State and explain two ways in which the glucose molecule is well suited to its function in
living organisms.
• Soluble → easily transported around body in the blood
- Quickly broken down → easy and quick release of ATP
• small molecule → can diffuse across cell membrane
- can form glycosidic bonds with adjacent glucose molecules via condensation reaction to form disaccharides/polysaccharides, e.g. maltose, lactose etc.
The cell walls of potato cells contain cellulose. Cellulose and starch are both carbohydrates. Describe two ways in which molecules of cellulose are similar to molecules of starch.
(2 Marks)
- Both are polymers
- Both joined by condensation reaction
- Both have 1-4 glycosidic links/bonds
- Both contain Carbon, Hydrogen and Oxygen
- Both insoluble
- Both contain glycosidic bonds
Describe the role of enzymes of the digestive system in the complete breakdown of starch
(5 Marks)
- Amylase enzyme
- hydrolyses glycosidic bonds in starch to produce maltose molecules
- maltose enzyme
- hydrolyses glycosidic bonds between maltose to produce alpha-glucose monomers
It is better to use a biosensor than the Benedict’s test to measure the concentration of glucose in a sample of blood. Suggest two reasons why.
(2 Marks)
- biosensor only detects glucose, whereas Benedict’s detects all reducing sugars
- biosensor gives quantitative readings, Benedict’s is semi-quantitative/qualitative
- biosensor is more sensitive - detects lower concentrations than Benedict’s
- biosensor can monitor blood-glucose concentration continuously
A drug company produced a new type of insulin. Scientists from the company carried out a trial in which they gave this new type of insulin to rats. They reported that the results of this trial on rats were positive. A newspaper stated that diabetics would benefit from this new drug. Suggest two reasons why this statement should be viewed with caution.
(2 Marks)
- study not carried out in humans
- sample size unknown
- long-term side effects not known
- study should be repeated to show repeatability - attainability of similar results
List three examples of where hydrogen bonds are found in biological molecules.
(3 Marks)
- cellulose
- DNA (complementary base pairs)
- 2/3 structure in proteins
- water (?)
State two roles of cholesterol in living organisms.
2 Marks
- regulate fluidity of phospholipid bilayer
- converted to steroid hormones, e.g. cortisol
- making Vitamin D
- making bile salts (?)
Two molecules that combine with cholesterol to form LDLs.
2 Marks
- proteins
- lipids/triglycerides
Name a disease that is caused by high blood cholesterol.
1 Mark
- atherosclerosis
- coronary heart disease/angina
Describe the structure and properties of carbohydrates that plants and animals use as energy stores. (6 Marks)
Animals:
Glycogen:
- made of alpha glucose monomers
- branched structure due to 1,6 glycosidic bonds
- branching enables glucose monomers to be easily snipped/hydrolysed off
- quick release of energy by respiration
- insoluble - doesn’t affect water potential
Plants:
Starch:
- amylose
- amylopectin
- both made of alpha-glucose monomers
