2.1.2 BIOLOGICAL MOLCULES Flashcards
MACROMOLECULES AND POLYMERS
monomer
small, basic molecular unit that makes a larger molecule i.e glucose
polymer
large, complex molecules made up of repeating monomers joined together i.e starch
macromolecule
complex molecules with relatively large molecular mass, made up of diff polymers/monomers i.e triglyceride(1 glycerol and 3 fatty acids)
condensation reaction
chemical process by which 2 molecules are bonded together to make a larger, more complex molecule with and eliminates a water molecule.
(basis for synthesising important macromolecules/proteins from sub-units)
Hydrolysis
breaks down chemical bond between monomers using a water molecule.
CARBOHYDRATES
carbs structure
polymers made up of carbon, hydrogen and oxygen (formula:Cx(H2O)y)
uses of carbs
-substrate for respiration to give energy(mainly glucose)
-storage of energy i.e glycogen/starch
-structural uses i.e cellulose makes up cell wall
monosaccharides
a repeating sugar unit, monomers that make up larger carbohydrates
glucose
hexose monosaccharide
has two isomers: alpha(OH group below) and beta(OH group above on condensation reaction side only) ABBA
USES: -main energy source in animals/plants(bonds have a lot of energy)
-soluble so can be easily transported, and respiration happens in cytoplasm which is aqueous (it is polar due to H bonds between hydroxyl groups and water molecules)
glycosidic bond
a covalent bond between a carbohydrate molecule and a hydroxyl group on another molecule, resulting from a condensation reaction
The 4 hexose monsaccharides
-galactose
-alpha glucose
-beta glucose
-fructose
ribose
-pentose monosaccharide
-sugar component of RNA nucleotide
Disaccharides
two monosaccharides joined together through condensation
1-4 glycosidic bond
type of covalent bond
glucose condensation reaction
-carbon 1’s (H) reacts with adjacent carbon 4’s (HO) to form waste water molecule.
form disaccharide
Maltose
(malt sugar) is formed from 2 glucose molecules joined together by an alpha 1-4 glycosidic bond.
Sucrose
(table sugar) is formed from a glucose and a fructose molecule(hexose monosaccharide) joined together by an alpha 1-6 glycosidic bond.
Lactose
(milk sugar) is formed from galactose and glucose joined together by an alpha 1=4 glycosidic bond.
Polysaccharide
more than two monosaccharides joined together
Starch
STRUCTURE: mixture of two polysaccharides of a-glucose=amylose and amylopectin
-stored as excess glucose by plants=can be broken down when needed for respiration
-insoluble in water so prevents water entering through osmosis and swelling up cell(doesn’t affect water potential)
-helical so compact
Amylose and Amylopectin
amylose: coiled , long, unbranched chain of a-glucose
-angles of alpha 1-4 glycosidic bonds give coiled structure–}good for storage as its compact. is soluble in water
amylopectin: straight , long, branched chain of a-glucose that is insoluble in water because it is a large molecule (alpha 1-4 and alpha 1-6 glycosidic bonds) 1-4 create coils and 1-6 create branches
-branches make it easier for enzymes to break down molecules so glucose can be released quickly for respiration
-helical so it can be tightly packed
-long molecule so it cannot cross plasma membrane
Glycogen
STRUCTURE: polysaccharide of a-glucose, similar to amylopectin with more side branches, created by high proportion of 1-6 glycosidic bonds (many ends for hydrolysing enzymes to attach)
PROPERTIES:
-compact so main energy store in animals for respiration
-branches release glucose quicker due to free ends
-can’t cross cell membrane because it is too large(good for storage bc it won’t escape cell)
-insoluble(doesn’t affect water potential of cell) so it won’t cause water to move in by osmosis
Cellulose
STRUCTURE: long, straight, unbranched chain of b-glucose arranged in layers
-beta 1-4 glycosidic bonds(every second B glucose is flipped so OH’s are adjacent)
-straight chains are linked together by many H bonds to form strong fibres (microfibrils, which together form macro fibrils)
-they make cellulose a good structural support/rigidity for cells
-permeable but doesn’t burst due to strength of cellulose cell wall
lipids
macromolecules that contain carbon, hydrogen and oxygen.
-NOT POLYMERS= just a mix of different, smaller molecules joined together
triglycerides
-made up of one molecule of glycerol with three fatty acid chains
-formed through 3 condensation reactions (waste product of 3 h20’s)
-esterification(type of con reaction) and 3 bonds formed are called ester bonds.
-large molecules due to long hydrocarbon chains
-non polar(insoluble in water), glycerol is polar but fatty acid chain is not
fatty acids
-RCOOH
-made up of carboxyl group, hydrocarbon chain(R) and methyl group
-bonds in hydrocarbon ‘tails’ are non polar so it is hydrophobic= make lipids insoluble in water
-high ratio of hydrogens and carbons to oxygens
-large due to its long hydrocarbon chains
-tail varies in each fatty acid
saturated fatty acids
-single bonds between carbons
-molecules have many contact points
-straight, parallel hydrocarbon chains can be tightly packed i.e solid animal fats
-higher melting point(solid)
-fully saturated with hydrogen(each carbon linked to a H molecule)
unsaturated fatty acids
-at least one double bond between carbons
-chain is ‘kinked’ so are not packed close together (fewer contact points) i.e plant oils
-lower melting point(liquid)
-not fully saturated with hydrogen because the number of double bonds reduces number of hydrogens present
-monounsaturated/polyunsaturated
Phospholipids
-outward facing hydrophilic head made up of a negatively charged phosphate group(polar) bonded to one molecule of glycerol
-head joined by ester bonds to tails
-inward facing hydrophobic tails repel water= two fatty acids
-makes a bilayer arrangement(oxygen in phosphate group has strong negative charge so polar and non polar regions is equal)
-may form oil droplets called micelle or bilayer
cholesterol
-hydrocarbon ring structure attached to a hydrocarbon chain
-ring has OH group attached to it
functions of cholesterol
-to strengthen cell membrane
-small, flat shape allows it to fit between bilayer and regulate fluidity
-stimulates formation of steroid hormones
-formation of bile
-Vitamin D synthesis
function of triglycerides
-short term energy storage(can be converted into glucose, chemical energy in C-C/C-H bonds)
-energy source through respiration(high ratio of H+C:O)
-more energy stores in less space(high energy value= low mass: energy ratio)
-thermal insulation to reduce heat loss (slow heat conductor)
-provide electrical insulation(some are wrapped around nerve cells to prevent escape of electrical impulses)
-insoluble (so prevent water swelling the cells and won’t affect water potential)
-too big to move across cell membrane
-buoyancy for aquatic animals(less dense than water)
function of phospholipids
-control movement of molecules
-centre of the bilayer repels water-soluble substances from easily passing through
-membrane acts as a barrier to those substances
-make cell surface membrane flexible(mix of saturated and unsaturated fatty acids)
-enable cell recognition(can form glycolipids)
Proteins
what are proteins made from?
-monomers= amino acid
-dipeptide: two joined together
-polypeptide: chain of more than two joined together
amino acid structure
-amino group
-variable region(gives amino acid it’s property)
-carboxyl group
-made up of C,H,O,N and S
how do amino acids join together?
-through a condensation reaction between OH group and H group with water produced
-produces peptide bonds(covalent bonds)
occurs in RIBOSOMES (hydrolysis occurs in digestive system)
primary structure
-sequence of amino acids in a polypeptide chain held together by peptide bonds
secondary structure
- H bonds form between amino groups and carboxyl groups= sections coil and fold
-coils= alpha helix
-folds= beta pleated sheets
(H bonds hold amino acids in place)
tertiary structure
-determines 3D shape of protein
R groups interact dependant on properties:
-H bonds form between slightly (+) Rs and slightly (-) Rs
-ionic bonds form between (-) Rs and (+) Rs(can hold parts of the polypeptide chain together)
-hydrophilic/phobic interactions
-disulfide bonds(type of strong covalent bond) between two cysteine molecules
quaternary structure
-more than one polypeptide chain(subunit)i.e haemoglobin
-determined by tertiary structure of the individual chains joining together to form a larger structure
-can also contain prosthetic groups that help the protein carry out its function(conjugated proteins)
Features of globular proteins
-spherical and (compact)
-soluble in water and easily transported: due to r groups that are attracted to water(hydrophilic) on their surface
Hydrophobic amino acids in centre of protein(complementary tertiary structure)
-temp sensitive
haemoglobin
-carries oxygen around the body in red blood cells
made up of 4 polypeptide chains each containing a haem group, 2 alpha and 2 beta subunits
* has an attached prosthetic group(inorganic component in a protein) haem(contains iron)
* so it’s a conjugated protein i.e glycoproteins, lipoproteins
* when oxygen attaches to haemoglobin changes quaternary structure making it easier for other oxygen molecules to bind onto haemoglobin
Insulin
- regulates blood glucose levels
-soluble: can be transported in the blood and diffuse through to the tissues where it acts
two polypeptide chains
• linked by disulphides bonds
• globular protein
• hormone
• shape of insulin molecule means that it complimentary to target cells
Amylase
-enzyme that catalyses the breakdown of starch in the digestive system
-made of single chain of AA folds to form a groove along surface(active site)
-secondary structure contains alpha helix and beta pleated sheets sections
-most enzymes are globular proteins
Fibrous proteins
-long tough and rope shaped molecules
-insoluble due to hydrophobic R groups
-structural proteins and fairly unreactive
Collagen
• found in animal connective tissues i.e bone,tendons, muscles and walls of arteries
• strong molecule due to structure
• forms a triple helix= 3 polypeptide chains wrap around each other in a tightly wound rope
•joined together by cross links + form microfibrils due to H bonds
• the molecule is staggered so there are no weak spots
• third amino acid is glycine which alleos collagen to wrap tightly making it strong
Keratin
-found in many external structure of animals i.e skin, hair, nails
- flexible/hard and tough due to fibrous shape
-insoluble
-high proportion of cysteine so have large number of disulfide bonds(very strong)
Elastin
-found in elastic connective tissue i.e skin, large blood vessels and some ligaments
-elastic so allows tissues to return to original shape due to fibrous shape
-long strands with hydrophobic regions that can form cross links and interact so they group together
WATER
STRUCTURE OF WATER
why is it a dipolar molecule?
-covalent bonds share electrons unevenly
(-) electrons move away from hydrogen and towards oxygen
what is a polar molecule?
has different charges across the molecule
how are hydrogen bonds formed?
-between o and h of adjacent molecules
slightly (-) oxygen attract the slightly (+) hydrogen of other water molecules
PROPERTIES
metabolite
-reactant in hydrolysis and photosynthesis
-produces in condensation reactions and respiration
how is water a solvent?
-dissolves hydrophilic polar molecules because it is polar(positive hydrogen will attract negative ion and negative oxygen will attract positive oxygen)
-transport medium: dissolved substances like glucose can be carried around
-medium for metabolic reactions: allows ionic compounds to separate
high specific heat capacity
-requires LOTS(4.18J) of energy to break the large volume of energy held in H bonds
-acts as buffer against rapid temp changes
-keeps internal environment of organisms stable and optimum enzyme conditions for aquatic animals
high latent heat of vaporisation
-lots of energy required to evaporate to gas because of H bonds
-cooling effect: sweat means heat energy transferred to surface and evaporates/ plants release water vapour in transpiration
strong cohesion
-the force of attraction between water molecules causing them to bond/stick together strongly and become very dense(surface tension)
can transport in continuous columns of water(capillary action)
-can become habitat to less dense organisms like pond skaters
importance of water being a solvent
-transport medium: dissolved substances like glucose can be carried around
-medium for metabolic reactions: allows ionic compounds to separate
-organisms can take in minerals
-able to dilute toxic substances
what is an ion?
atom or group of atoms that have an electrical charge
inorganic ions
doesn’t contain carbon
Calcium(ca2+)
-transmission of nerve impulses and release of insulin from the pancreas
-acts a cofactor(non-protein compound required for enzyme activity)
sodium(Na+)
-important for generating nerve impulses, for muscle contraction and regulating body fluid balance
potassium(K+)
-same as sodium
-activates essential enzymes for photosynthesis
hydrogen(H+)
-affects pH of substances(more h=more acidic)
-important for photosynthesis and respiration
ammonium(NH4+)
-important source of nitrogen for plants (used to make amino acids, nucleic acids)
nitrate(NO3-)
-same as ammonium
hydrogencarbonate(HCO3-)
-buffer that helps maintain the pH of the blood
chloride(Cl-)
-‘chloride shift’ maintains pH of blood during gas exchange
-cofactor for amylase
-involved in some nerve impulses
phosphate(PO(4)3-)
-involved in photosynthesis and respiration reactions
-needed for synthesis of many biological molecules i.e phospholipids, nucleotides
hydroxide(OH-)
-affects the pH of substances(more OH=more alkali)
BIOLOGICAL TESTS
What is qualitative testing?
non-numerical, observation based testing
The biuret test for proteins
-add a few drops of sodium hydroxide solution to make solution alkaline
-add some copper(II) sulfate solution
-positive result=blue to purple
(detects peptide bonds, if it was just amino acids it wouldn’t turn purple)
The iodine test for starch
-add sample to test tube
-mix in a few drops iodine dissolved in
potassium iodide
solution
-positive result=brown-orange to
blue-black
(iodine separates out of solution and binds to the coiled chains of starch)
*starch cannot be detected with benedict’s due to the minimal amount of reducing sugar molecules found only at the ends of carbohydrate chains
The emulsion test for lipids
-add around 2cm3 of UNFILTERED food sample to test tube(dry and grease free)
-Add around 5cm3 of ethanol into sample and shake it
-pour solution into around 5cm3 of water
-positive result= solution forms a milky emulsion
(becomes emulsion because non polar region of lipids form micelles in water and shaking tube makes even smaller micelles and are distributed through water)
What are reducing sugars?
sugars that donate electrons or reduce another molecule i.e all monosaccharides and lactose and maltose
Bendict’s test for reducing sugars
(benedicts is an alkaline solution of cu II sulfate)
-grind sample with water
-Add Benedict’s
reagent to the sample (same volume as original mixture) and
gently heat in a water bath for around 5 mins
- positive result= blue to brick red/orange brown precipitate
-due the addition of electrons to the blue Cu2+ ions reducing them to brick red Cu+ ions(can be green, yellow, orange then brick red)
Benedict’s test for non-reducing sugars
-confirm it is non-reducing by doing ordinary benedicts
(now break down poly/disaccharide to a monosaccharide)
-grind up sample and put in test tube with water
-boil with a few drops HCl for around 5 mins
-Neutralise with a few drops of
sodium hydrogen
carbonate and use pH paper to check if it is alkaline(benedict’s can’t work in acidic conditions)
-Do Benedict’s Test
for reducing sugars.
-positive result= blue to brick-red
Test strip for glucose
-Dip test strip in
solution
-Colour change will occur
if glucose is present
-Compare to chart of
known colour changes to
check for concentration
What is quantitative testing?
numerical testing
Colorimetry benedicts test for sugars
-make reducing sugar solutions of known concentrations using serial dilution technique
-do a benedicts test on each solution + one water test tube(blue to brick red)
-select the red filter on the colorimeter
- calibrate using a cuvette ¾ filled with distilled water
-use pipette to fill the cuvette ¾ with each sample and read the absorbance of light
-plot absorbance against known conc in calibration curve to find conc
biosensors
-device that uses a biological molecule to detect a chemical
-produces a signal which is converted to an electrical signal by a transducer
-processed and can be used to work out further info
TLC
-Grind up the leaves using a pestle and mortar, with some anhydrous sodium
sulphate and then add some propanone as a solvent
-Draw a line on the TLC plate(made of silica gel) with a pencil about 2cm from the bottom
-pipette some pigment and place in the middle of pencil line(wait till dry and keep going over the spot)
-Add a small amount of solvent in a beaker(below pencil line)
-mark the solvent front and the pigment spots(might fade)
What is Rf value?
distance of pigment/solvent
why is Rf important?
-can be compared to a standard value in a database to identify the pigment
Adhesion in plants
-when water molecules are attracted to the impermeable walls of xylem tissue
-the force of attraction between water and surfaces it is in contact with—> makes water molecules tend to stick to other things
how to tell what glycosidic bond it is on a diagram
-count the first molecule’s carbons clockwise and the second inverted
- 1-6 bond would be one molecule on top of the other because the 6th carbon is in the CH20H part
Why can alcohol dissolve non polar substances like triglycerides and phospholipids?
-has both polar AND non polar regions so can mix with both types of regions
Protease
-catalases the breakdown of peptide bonds between amino acids
-soluble in water so it is able to diffuse through the cell and bind to its specific substrate
