2.1.2 Biological molecules Flashcards
how polarity in water is formed (biology)
O pulls pair of electrons in covalent bond closer to it and further from H as has more protons
O has partially negative charge
H has partially positive charge
properties of water
polar liquid at room temperature high specific heat capacity (SHC) high latent heat of vaporisation (LHV) high cohesion/adhesion high surface tension water is denser than ice not compressible (liquid)
roles of water for living organisms
site of chemical reactions (solvent)
stable enzyme-controlled reactions (high SHC)
allows molecules and ions to be transported easier in living things (solvent)
stable environment of aquatic organisms (high SHC and LHV)
columns of water pulled up by xylem vessels (adhesion due to hydrogen bonding)
important metabolite (photosynthesis, hydrolysis)
monosaccharide definition
sugar monomer
carbohydrate uses
source of energy (glucose)
store of energy (starch, glycogen)
structural unit (cellulose cell wall, chitin cell wall of fungi)
monosaccharide properties
sugars (sweet)
soluble in water
insoluble in non-polar solvents
reducing sugars examples
maltose
lactose
all monosaccharides
non-reducing sugars
most disaccharides (e.g. sucrose)
how disaccharides are formed
condensation reaction to form glycosidic bond between two monosaccharides
monosaccharides of maltose
alpha-glucose + alpha-glucose
monosaccharides of sucrose
alpha-glucose + fructose
monosaccharides of lactose
beta-galactose + beta-glucose
monosaccharides of cellobiose
beta-glucose + beta-glucose
how polymers are formed and broken down
condensation reaction (release water molecule) hydrolysis reaction (requires water molecule)
starch structure
only alpha-glucose
amylose + amylopectin
amylose structure
long
coiled (hydroxyl bonds create hydrogen bonds to maintain structure)
unbranched (1-4 glycosidic bonds only)
good for storage (compact)
amylopectin structure
long
also coil due to hydrogen bonds
branched due to 1,6-glycosidic bonds
more accessible ends for enzymes for faster hydrolysis into alpha-glucose
properties and function of starch
major carbohydrate storage molecule in plants
stored as intracellular starch grains (plastids)
produced from glucose made in photosynthesis
broken down during respiration for energy
insoluble so doesn’t affect water potential
glycogen structure
long
highly-branched (many 1,6 glycosidic bonds)
more accessible ends to enzymes (more than amylopectin) so faster hydrolysis into alpha-glucose
glycogen function and properties
main energy storage in animals
more glucose residue branches so energy is released quickly (animals have higher metabolism than plants)
stored in liver and muscles
less soluble, more compact than starch (animals have higher metabolism than plants)
cellulose structure
beta-glucose orientated 180° to form straight chains (prevent coiling)
1-4 glycosidic bonds
hydrogen bonding between adjacent chains to form microfibrils (more tensile strength)
bundles to form macrofibrils that criss-cross (more tensile strength)
cellulose cell wall features and role
tough, insoluble
hard to digest (strong glycosidic bonds, most animals lack necessary enzymes)
high tensile strength (glycosidic bonds, hydrogen bonds between chains) so doesn’t burst when turgid, support whole plant
permeable (gaps between macrofibrils)
can be reinforced (e.g. lignin, cutin)
other structural polysaccharides
peptidoglycan (bacterial cell wall, arranged similarly to cellulose)
chitin (exoskeleton of insects and crustaceans, fungi cell wall, arranged similarly to cellulose)
lipid general features
non-polar
insoluble in water, dissolve in alcohol
less dense than water
soluble in non-polar solvents
glycerol structure
3 carbon molecules 3 hydroxyl (-OH groups) attached to carbons
fatty acid structure
carboxyl group (-COOH)
attached to hydrocarbon tail (2-20 carbons long)
acid as can dissociate H+ ions
can have saturated or unsaturated hydrocarbon tail
effect of double bond on hydrocarbon tail
creates “kink” at double bond
pushes molecule slightly apart
reduces intermolecular interactions between molecules so more fluid, lower MP
triglyceride structure
1 glycerol bonded to 3 fatty acids
by ester bonds formed in condensation reactions
ester bond
bond formed between fatty acids (or phosphate group) and triglyceride
formed between carboxyl group (-COOH) of fatty acid and hydroxyl group
between hydroxyl groups for phosphate
released water molecule per bond
esterification reaction
functions of triglycerides
energy source (broken down in respiration to provide ATP, releases around double energy than carbohydrates)
energy store (insoluble so doesn’t affect water potential of adipose tissue)
insulation (heat insulator e.g. blubber, electrical insulator on nerve cells)
buoyancy (less dense than water)
protection (can absorb shock when surrounds organs)
phospholipid structure
1 glycerol bound to 2 fatty acids, 1 phosphate group by ester bonds
hydrophilic phosphate head (as negative charge)
hydrophobic fatty acid tails
amphiphatic
behaviour of phospholipids in watee
hydrophilic phosphate heads face towards regions of water
hydrophobic fatty acid tails turn away from regions of water
forms bilayer or micelles
micelle definition
hydrophobic tails inside structure
hydrophilic heads facing outwards towards regions of water
sterols definition
complex alcohol molecules based on 4 carbon ring structure with hydroxyl group at one end (-OH) e.g. cholesterol
cholesterol structure
steroid nucleus (4 carbon rings)
hydroxyl group at one end
hydrocarbon side chain at other end
cholesterol functions
manufacture in liver and intestine
formation + stability of plasma membrane
synthesis of steroid hormone
can pass through plasma membrane because small + hydrophobic
amino acid definition
monomers of all proteins
all have same basic structure
protein functions
structural: muscles add of protein, whore
catalytic: form enzymes
carriers and pores: carrier and channel proteins of plasma membrane
amino acid general structure
carboxyl group
amino group
central hydrogen
varying R group
buffer definition
substance that helps to resist large changes in pH
how amino acids join and break up
condensation reaction
forms peptide bond (OCHN) between amino group of one amino acid and carboxyl group of another amino acid
release water
hydrolysis reaction
breaks peptide bond
requires water
forms 2 amino acids
primary structure definition
sequence of amino acids in a polypeptide chain
secondary structure definition
coiling or folding of peptide chain to form alpha-helices or beta-pleated sheets due to hydrogen bonding
why primary structure is important
determines shape of molecule (determines secondary, tertiary, quaternary structure)
many possible sequences so gives each enzyme a unique shape and specific function
how alpha-helices form
peptide chain coils
held by hydrogen bonds that form between -NH group and -CO group of different amino acids
how beta-pleated sheets form
chains fold over on itself slightly to form zig-zag structure
hydrogen bonds form between -NH and -CO groups of different amino acids
tertiary structure definition
overall 3D shape of protein molecule due to hydrogen bonding, disulphides bridges, ionic bonds and hydrophobic interactions
between R groups of amino acids
quaternary structure definition
how multiple polypeptide chain subunits come together
only in complex proteins e.g. haemoglobin, insulin
hydrogen bonds in tertiary structure
between carboxyl, hydroxyl and amino groups
between R groups of amino acids
ionic bonds in tertiary structure
carboxyl and amino groups in R group ionise into COO- and NH3+ respectively
oppositely charged ions strongly attracted to each other to form ionic bond
disulfide bridges in tertiary structure
R group of cysteine has sulfur
strong covalent bonds form between sulfur on R groups of 2 cysteine amino acids
hydrophobic/philic interactions in tertiary structure
hydrophobic parts tend to associate together at centre of polypeptide to avoid water
hydrophilic parts found at edge of polypeptides close to water
both causes twisting and changing of polypeptide chain’s shape
fibrous proteins features
regular, repetitive sequence of small range of amino acids
insoluble in water
long chain
thin structure
has structural function (e.g. collagen, elastin)
little/no tertiary structure
globular protein features
relatively spherical shape
soluble in water
have very specific shape
often have metabolic roles (enzymes, hormones, haemoglobin)
collagen properties and functions
mechanical strength (lots of hydrogen bonds)
collagen around arteries to prevent from bursting
tendons, cartilage and connective tissue made out of collagen
bones made out of collagen then reinforced with calcium phosphate
keratin properties and functions
lots of cysteine so more disulfide bonds
makes it strong
provides mechanical protection, impermeable barrier to infection, waterproof
found in nails, hair, claws, hooves, forms, scales, fur, feather (anywhere hard)
elastin properties and features
cross-linking + coiling so strong and extensible
found in skin, lungs, blood vessels (anything that needs to change its shape and stretch)
haemoglobin structure, properties and functions
two alpha and 2 beta globin chains
each chain holds a prosthetic haem group (Fe2+)
conjugated protein
oxygen molecule binds to iron ions in haem groups and gets released at tissues
insulin structure, properties and functions
2 polypeptide chains (A and B) joined by disulfide bridges
A chain begins with alpha helix
B chain ends with beta pleated sheet
hydrophilic R groups on outside of molecule so is soluble
binds to glycoprotein receptors (muscle, fat cells) to increase intake and consumption of glucose from blood
pepsin structure, properties and functions
single polypeptide chain folded into symmetrical tertiary structure held by hydrogen bonds and disulfide bridges
made up of 43 AA with acidic R groups
few basic groups to accept hydrogen ions
so low pH has little effect on structure
Ab initio (in italics) protein modelling
protein model is built based on physical and electrical properties of atoms in each amino acid in sequence
multiple solutions can be made
other methods required to deduce real structure of protein
comparative protein modelling
protein threading (scans a amino acid sequence against related proteins with known structures) produces set of possible models
Ca 2+ functions
involved in transmission of nervous impulses regulating of protein channels muscle contractions hardening of teeth and bones
Na + functions
involved in
transmission of nervous impulses
active transport Na+ pump
co-transport of glucose and amino acids across membranes
K + functions
Involved in
transmission of nervous impulses
active transport
plant cell turgidity
H + functions
The higher the concentration, the lower the pH of bodily fluids
NH4 + functions
Source of nitrogen used to make organic molecules
NO3 - functions
Source of nitrogen used to make organic molecules
HCO3 - functions
Involved in the regulation of blood pH and transport of carbon dioxide in the blood
Cl - functions
involved in
transport of carbon dioxide in the blood through the chloride shift
production of hydrochloric acid
allosteric effect
binding of ligand to one site of protein molecule so properties of another sire on same protein molecule are affected
ligand meaning
ion or molecule that binds to another (usually larger) molecule
PO4 3- functions
Component of biological molecules such as nucleotides, ATP and the formation of the phospholipid bilayer
OH - functions
The higher the concentration, the higher the pH of bodily fluids
deficiency definition
when organism doesn’t have enough of a particular inorganic ion
test for starch
add iodine dissolved in potassium iodide to sample
positive if yellow-brown turns blue black
triiodide ions slips into middle of amylose helix, causes colour change
test for reducing sugars
add Benedict’s solution in excess (alkaline copper (II) sulfate)
heat in water bath (80°C, 3 minutes)
positive if colour change from blue to brick-red and anything in between
blue Cu 2+ ions turn into brick red Cu + ions as are donated electrons from reducing sugars
test for non-reducing sugars
test for reducing sugars first
take separate sample and boil with hydrochloric acid (hydrolyse to form monosaccharides)
cool solution, neutralise using hydrogencarbonate solution
test for reducing sugars again
positive if only second test has colour change
test for lipids
mix sample throughout with ethanol
filter and pour solution into water in clean test tube
positive if cloudy white emulsion forms
tiny lipid droplets come out of ethanol solution when mixed with water
test for proteins
add biuret A (sodium hydroxide)
add biuret B (copper sulfate)
positive if lilac-colour formed
complex formed between Cu 2+ and nitrogen atom in peptide chain
quantitative test for reducing sugar
conduct reducing sugar test with excess Benedict’s solution
separate unreacted Benedict’s solution using centrifuge
collect supernatant using pipette and place into cuvette
place (red) colour filter into colorimeter
calibrate colorimeter using distilled water
test supernatant with colorimeter
less transmission / more absorption = more unreacted copper sulfate solution = less reducing sugar
more transmission / less absorption = less copper dilate solution = more reducing sugar
creating calibration curve
carry out Benedict’s test on samples of known concentrations of reducing sugar
separate Benedict’s solution from each sample with centrifuge
use colorimeter and record percentage transmission of light through each supernatant
plot graph (transmission of light against glucose concentration) and draw line of best fit
can estimate glucose concentration of unknown samples with transmission readings
biosensor definition
takes biological or chemical variable hard to measure and converts it into electrical signal
biosensors general mechanism
molecules to be measured bind to biological layer via receptors
transducer surface creates electronic signal
signal conditioner creates an output
stationary phases
chromatography paper (made of cellulose) or thin-layer chromatography plate (sheet of plastic coated with thin layer of silica gel or aluminium hydroxide)
mobile phase
solvent that carries biological molecules
flows through and across stationary phase
how chromatography works
solvent moves up stationary phase, carrying soluble pigments with it
pigments move at different speeds (due to polarity, size, solubility in solvent)
more polar = stick to the stationary phase more = slowly and vice versa
relative distance (chromatography) formula
Rf = x/y Rf = relative distance travelled by a pigment x = distance between CENTRE of spot of pigment and pencil line y = distance between solvent and pencil line
how to spot colourless molecules in chromatography with UV light
TLC plates have chemical that fluoresces under UV light, colourless pigment will mask plate from UV light so no glowing
how to spot colourless molecules in chromatography with ninhydrin
allow plate to dry
spray with ninhydrin
binds to amino acids, become visible as brown or purple spots
how to spot colourless molecules in chromatography with iodine
allow plate to dry
place in enclosed space with few iodine crystals
gas formed from iodine binds to molecules in each spot
uses of chromatography
monitor progress of reactions (as it is quick)
analyse for illegal drugs in urine of athletes, purity of components of drugs, contaminants in food
reducing sugar disaccharides
lactose
maltose
cellobiose