Biological Molecules Flashcards
Why is water polar? Draw it with another water molecule
The oxygen atom in a water molecule is more electronegative than the hydrogen atom so it becomes slightly negative charged and the hydrogen molecule slightly positively charged. There is an unequal charge distribution across the molecule so it is polar.
Name all the properties of water that make it important
Density, solvent, cohesion, high specific heat capacity, high latent heat of vaporisation, reactant
Explain density and solvency’s role for living oragnisms
Density - ice is less dense than water (molecules spread out in a lattice) so it floats and forms insulating layer, still swim/nutrients can still circulate
- stable environment to live in winter
- lakes/ponds are insulated against extreme cold
Solvent - ionic solutes, water is attracted to + - parts. Keep them apart so they dissolve
- molecules and ions can move around and react in water (cytoplasm)
- molecules and ions can be transported (medium eg blood) dissolved in a pond
- dilute toxic substances
Explain cohesion and reactant’s role for living organisms
Cohesion - hydrogen bonding allows molecules to stick together creating surface tension. Can stick to other surfaces. This results in capillary action.
- columns of water in plants vascular tissue is pulled up
- insects walk on water
Reactant - water takes part in some chemical processes
- photosynthesis and hydroysis
- medium for metabolic reactions
Explain thermal stabilitys role for living organisms
High specific heat capacity - heat energy released, need alot of energy to overcome hydrogen bonds, doesn’t heat up or cool easily
- living things need stable temp for reactions to take place
- aquatic organisms
High latent heat of vaporisation - heat energy that helps molecules break away from each other to become a gas, large amount of energy is needed for evaporation
- mammals are cooled when sweat evaporates
- plants cool water evaporates off leaves
- bodies of water don’t evaporate away every summer
Write how 4 disaccharides are formed
a glucose + a glucose = maltose
a glucose + fructose = sucrose
b galactose + a glucose = lactose
b glucose + b glucose = cellobiose
Describe a condensation reaction
Two hydroxyl groups line up next to each other, from which a water molecule is removed. Leaving an oxygen atom acting as a link between the two monosaccharides. Called a glycosidic bond.
Describe a hydrolysis reaction
The addition of water provides a hydroxyl group and a hydrogen, which breaks the glycocidic bond.
What are the functions of a carbohydrate?
- energy source (glucose)
- energy store (starch)
- structure (cellulose)
Draw glucose and cellulose and include an explanation of how they’re different
In a glucose there the hydrogen group on the first carbon is above the hydroxyl group. In b glucose the -OH group on 1st carbon is above the hydrogen group. The hydrogen and hydroxyl groups in B glucose compared to a glucose, are inverted 180 degrees
Draw a table with a glucose, B glucose, ribose and deoxyribose in it with displayed and molecular formula, role in the body and type of sugar
a glucose C6H12O6 energy source, component of starch and glycogen (energy stores) hexose
B glucose C6H12O6 energy source, component of cellulose provides structural support in plant walls hexose
Ribose C5H10O5 component of ribonucleic acid RNA, ATP and NAD pentose
Deoxyribose C5H10O4 component of deocyribonucleic acid DNA pentose
Explain why polysaccharides are good energy stores
- Compact - dense granules
- Easy hydrolysis - chains allow this when required for respiration
- Branched - compact and allow more glucose molecules to be hydrolysed at the same time
- Insoluble - doesn’t disrupt water potential, due to size and hide regions that could hydrogen bond with water (double helix presents hydrophobic surface)
Explain amylose
Found in plants. Storage. Long chain of glucose attached by 1-4 glycosidic bonds. Coils into spiral shape with hydrogen bonds holding it in place. OH group on carbon 2 is outside coil making it less soluble.
Explain amylopectin
Found in plants. Storage. Like amylose but also with branches formed by glycosidic bonds between carbon 1 and 6. Coils into a spiral shape held together by hydrogen bonds with branches emerging from the spiral.
Explain glycogen
Found in animals. Storage. Like amylopectin with 1-4 and 1-6 glycosidic bonds. 1-4 bonded chains are smaller than amylopectin so less tendency to coil. Has more branches so more compact and easier to remove monomer units as there are more ends.
What is glucose’s function?
- respiratory substrate
- energy source
- formation of ATP
- energy storage (amylose)
State and explain ways in which glucose is suited to its function
- soluble easily transported
- small diffuse across membranes
- easily respired to release ATP
- can join to make di and poly saccharides
Why doesn’t cellulose spiral like chains of a-glucose?
H and Oh groups on carbon one are rotated 180 degrees compared to a glucose. The B 1-4 + that helps stop spiralling.
Hydrogen bonding between the B molecules gives chain strength and stops it from spiralling.
Hydrogen bonding between rotated B glucose molecules in different chains gives whole structure additional strength. H bonding due to the OH group sticking out on carbon 2.
Suggest 3 reasons why cellulose is an excellent material for plant cell walls
- Microfibrils and macrofibrils (embedded in pectin) have very high tensile strength = glycosidic bonds and hydrogen bonds
- Macrofibrils run in all directions criss-crossing the wall for extra strength
- Difficult to digest cellulose because glycosidic bonds between B glucose are less easy to break
Suggest 3 reasons that help the plant cell wall do its job
- There is a place between macrofibrils for water and mineral ions to pass in and out of cell = fully permeable
- wall has high tensile strength which prevents plant cells from bursting when they are turgid = supports whole plant, also wall protects cell membrane
- macrofibrils can be reinforced with cutin, suberin and lignin to waterproof it, trunks need extra thick walls to withstand weight
List material that humans use that are based on cellulose for its structural strength
Cotton, cellophane, celluloid, paper, rayon
Describe how bacterial cell walls are structured
Made from peptidoglycan. Made from long polysaccharide parallel chains cross linked by short peptide chains
Describe how insect and crustacean exoskeletons are structured
Made of chitin. It has a acetylamino group rather than a hydroxyl group on carbon 2. Forms cross links between parallel chains of acetylglucosamine.
What are lipids?
Contain C, H and some O. Insoluble in water bc not polar but do dissolve in alcohol. Macromolecules not polymers because they don’t contain monomers.
Draw glycerol and a fatty acid and explain why it is an acid
The carboxyl group ionises into H+ and a -COO- . Acid because it can produce free H+ ions.
What does saturated mean and what effect does this have? Give some examples of unsaturated carbons
Saturated means no C=C bonds. Unsaturated means there is a double bond between 2 of the carbon atoms. Having 1+ C=C bonds gives it a kink in the chain where the C=C bond is. The kink pushes the molecules slighly apart, making them more fluid.
Animals contain saturated=solid at 20 C
More unsaturated=melting point is lower
Eg. 1 C=C monosaturated oleic acid
1+ C=C polysaturated linoleic acid
Draw the formation of an ester bond and label
Should include: condensation reaction between the COOH on fatty acid and OH on glycerol. Shows 3 bonds. Labels ester bond (covalent). Label the condensation reaction H2O eliminated. Hydrolysis reaction H2O used up.
List the 5 functions of triglycerides and explain them
- energy source - can be broken down in respiration to generate ATP. Hydrolyse the ester bonds and then glycerol and fatty acids can be broken down into CO2 and H2O
- energy store - insoluble so don’t affect water potential, animals store fat in adipose cells (lipids have higher H2 than glucose + no O2))
- insulation - adipose acts as heat insulator. Nerve cells have electrical insulator
- buoyancy - less dense than water used to aquatic to stay afloat
- protection - humans have fat around delicate organs to act as shock absorber (petidoglycan is sometimes covered in lipid rich coat)
What is the difference between a triglyceride and a phospholipid? Draw
Same structure as triglycerides expect one of the fatty acids is replaced by as phosphate group H3PO4. Condensation reaction between an OH group on phosphate and one of OH on glycerol. Ester bond. Macromolecule.
Explain and describe phospholipids behaviour in water
H3PO4 has a negative charge making in polar. Fatty acid tails are non polar so are repelled by water. Hydrophilic head and hydrophobic tail. It is amphipathic. Storage lipids aren’t.
They form a layer on surface of water with heads in the water and tails sticking out of water. Also form micelles; tails inside, heads pointing outwards.
Explain what the phospholipid bilayer is
2 rows of phospholipids tails pointing inwards, heads pointing outwards.
- phospholipids can move around in the layer but won’t move to where the tails are exposed to water = stability
- selectively permeable, only small, non polar molecules can go through CO2 and O2 = it can control
Explain the structure of cholesterol and its function
Steroid alcohol. Consists of 4 isoprene units. Small hydrophobic molecule can sit in the middle of the hydrophobic part of bilayer. Regulates fluidity of membrane.
Made in the liver. Plants have stigmasterol.
Oestrogen, vitamin D, testosterone made from cholesterol. Small and hydrophobic they can pass through bilayer.
Explain and describe the roles of phospholipids, glycolipids and cholesterol in the plasma membrane
Phospholipids create a barrier between the inside of the cell and the environment.
They prevent large, polar molecules passing through the layer.
Glycolipids aid in cell signalling/ recognition on cell surface
Cholesterol stabilises plasma membranes and prevents them from freezing.
Draw the structure of an amino acid and give some examples
Drawn with the carboxylic acid and amine group, H and R group.
Cystiene CH3S, alanine CH3, glycine H
Why is it said that amino acids are buffers
The NH2 and COOH groups can ionise in water. The NH2 group can accept H+ and the COOH can give up H+ changing them from NH3+ and COO-. Amine is a base and the COO- is an acid.
They are amphoteric.
They can resist large changes pH
Draw the condensation of a peptide bond being formed and the hydrolysis for one being broken. Give an explanation for this
Drawn.
The bond is between amine group of one amino acid and carboxyl group of another
H of amine combines with OH of carboxyl to form water
Water is eliminated = condensation reaction
and vice versa
Describe the primary structure of an amino acid chain
The sequence of amino acids in a protein chain. Changing an amino acid in the chain can alter the function of the protein. The function of the protein is determined by its structure through its secondary, tertiary and quaternary structure.
Describe the secondary structure of a chain of amino acids with reference to hydrogen bonds
Some chains aren’y straight.
A-helix, held together by hydrogen bonds between the -NH group of one amino acid and the -CO group of another
B-pleated sheet, hydrogen bonds between the -NH group of one amino acid and the -CO group of another down the strand
Hydrogen bonds are relatively weak, many are formed which makes them both stable at op temp and pH
Describe the tertiary structure of a chain of amino acids
The coils and pleats start to fold with straight chains. Very precise, held firmly together. Could be supercoiled (fibrous) or spherical (globular)
Describe the 4 ways proteins bond and draw them
Hydrogen bonds - form between NH2, OH, COOH groups, they may also form between polar areas of R groups, keeps tertiary and quaternary structures in plave, with strength
Ionic bonds - form between COOH and NH2 that are part of R groups, NH3+ and COO- ionise and attract
Disulfide links - R group of cystiene contains sulfur, form strong covalent bonds
Hydrophobic/philic interactions - phobic parts associate in the centre of the polypeptide to avoid water (philic found edge etc) They cause twisting of the amino acid chain, which changes shape
Describe the function and structure of fibrous proteins: collagen
To provide mechanical strength
- artery walls prevent bursting when withstanding high pressures
- tendons connect to bones allow them to pull on bones
- bones collagen and reinforced with Ca3PO4 that makes them hard
- cartilage and connective tissue
Describe the function and structure of fibrous proteins: keratin
Found where the body part needs to be hard, providing mechanical protection, impermeable barrier to infection, waterproof and prevents entry of waterbourne pollutants
- finger nails, claws, hoofs, horns, scales, fur, feathers
Rich in cystiene so many disulfide bridges form between the chains. + h-bonds makes it VERY strong
Describe the function and structure of fibrous proteins: elastin
Found where the body needs to stretch or adapt their shape
- skin can stretch around our bones and muscles
- lungs allows inflate and deflate
- bladder expand to hold urine
- blood vessels stretch and recoil helps maintain pressure
Cross linking and coiling make it strong and extensible
Describe the function and structure of globular proteins: haemoglobin
Quaternary structure made of 4 polypeptide subunits: 2 a-globin chains and 2 B-globin chains all bonded by protein bonds (explain)
On the outside of each chain there is a space where a haem group is held; prosthetic groups, each haem contains an iron ion, called a conjugated protein
Function: carry oxygen from the lungs to the tissues, in lungs O2 binds to binds to Fe2+, turns from purple to bright red, O2 released at tissues
Describe the function and structure of globular proteins: insulin
Made from 2 polypeptide chains. A chain begins with a-helix and the B chain ends with B-pleated sheet. Both are tertiary structures joined by a disulfide link. Philic R groups are outside which makes in soluble in water
Insulin binds to glycoprotein receptors on outside of muscle and fat cells increase uptake of glucose from the bloodand increase rate of consumption of glucose
Describe the function and structure of globular proteins: pepsin
It is made from a chain of 327 amino acids, folds into symmetrical tertiary structure, it has 43 acidic R groups,, it is very stable in the stomach acid because there are so few basic groups to accept H+ ions, held together by hydrogen bonds and 2 disulfide bridges
How to test for starch
Add iodine solution (KI). Yellow-brown to blue-black.
I2 = I3- slips into the amylose helix
How to test for reducing sugar and what does reducing mean?
Reducing sugars = give electrons to other molecules
Heat sugar with Benedicts solution. 80 C for 3 mins. Blue to green to yellow to orange-red.
Cu2+ = Cu+ form Cu2O red. Called precipitate
How to test for non reducing sugars
They don’t give electrons to other molecules
Hydrolyse bond first. Then test for reducing sugars.
- first test for reducing sugars
- take separate sample and boil it with HCl to hydrolyse into glucose and fructose
- cool the solution and use NaHCO3 to neutralise
- test for reducing sugars again
Extract precipitate by filtration
How to test for lipids
- mix thoroughly with ethanol, any lipid will go into solution in ethanol
- filter
- pour the solution into water in a clean test tube
- cloudy white emulsion indicates the presence of lipids (tiny lipid droplets that come out of solution when mixed with water)
How to test for proteins
Biuret test, light blue to lilac. Biuret A (OH) and biuret B (Cu2SO4).
Nitrogen in peptide chain and Cu2+ ions = tests for peptide bonds
Describe how to use a colorimeter
Centrifuge the precipitate and excess Benedict’s solution (supernatant)
- use pipette to take the supernatant and put into a curvette and place into the colorimeter (be careful with greasy fingerprints as this affects transmission of light)
- shine a light, red through the solution it will detect how much light passes through (percentage transmission)
- less unreacted Cu2SO4, the supernatant is less blue so absorption of red light is low so high % transmission
Why is it important to zero the colorimeter?
The device must be zeroed between each reading to reset the 100% transmission, water is used. This will mean the results are are comparable and the readings are measuring correctly
Explain how you would create a calibration cure
- take a series of known concs of reducing sugars
- using sample of each, do Benedicts test
- use colorimeter to record % transmission
- plot a graph to show ‘transmission of light’ against the concentration of reducing sugar (g dm-3), provides a calibration curve, compare
Why use a biosensor?
It is used when a variable can’t easily be measured so you can convert it into an electrical signal.
Detect contaminants in water, pathogens and toxins in food, airbourne bacteria
Describe briefly how a biosensor works
Molecules are released and bind at the receptor on the biological layer (the binding event). At the transducer surface, an eletrical signal is released and sent to the elctronics (signal conditioner) which results in an output
What is the stationary and mobile phase?
Chromatography paper (celluose) or TLC (sheet of plastic coated with thin layer of silica gel) Free -OH groups pointing outwards
Solvent, water for polar and ethanol for non polar, flows across stationary phase
Describe the chromotography practical and the considerations
- wear eye protection
- draw the line in pencil (ink will also separate) put a small dot on the line to show where to place the solution mixture
- spot the mixture onto the dot serveral times with capillary tubing, wait for dot to dry, try to make it as thin as possible
- when dry lower it into the solvent below the pencil line
- cover beaker with a watch glass
- let the apparatus run until it has reached the top
- remove from the solvent and lay it on white tile to dry
Describe how chromotography works, what it is used for and give the formula
The components of solution travel with solvent. Each have different speeds so they will appear at different positions. The speed up depends on the solubility in solvent and the polarity (paper; size)
- exposed OH groups make the surface polar so will form hydrogen bonds
- highly polar solute will stick and move slowly and a non polar will move very quickly
- if same speed change pH or solvent
Used for: urine testing athelets, analysing drugs for purity, analysis of foods to determine contaminants
Rf = x/y (x=dye and y=solvent)
What 3 solutions can you use to see colourless molecules?
- UV light TLC (spots won’t glow)
- Ninhydrin to see amino acids spray to see brown dots
- Iodine contain with crystal form gas and bind to molecules
