biological molecules Flashcards
condensation reaction definition
reaction that occurs when two molecules are joined together with the removal of water
hydrolysis reaction definition
reaction that occurs when a molecule is split into 2 smaller molecules with the addition of water
monomer definition
a small molecule which binds to many other identical molecules to form a polymer
polymer definition
a large molecule made from many smaller molecules called monomers
hydrogen bond definition
a weak interaction that can occur whenever molecules contain a slightly negatively charged atom bonded to a slightly positively charge hydrogen atom
where can hydrogen bonds form?
between chains of monomers
are hydrogen or covalent bonds weaker?
hydrogen bonds
what is a macromolecule?
a large molecule
4 examples of macromolecules
carbohydrates, proteins, nucleic acids, lipids
carbohydrate chemical elements
carbon, hydrogen and oxygen
carbohydrate monomer
monosaccharide e.g. glucose
carbohydrate polymer
polysaccharide e.g. glycogen
protein chemical elements
carbon, hydrogen, oxygen, nitrogen ( and sulfur )
protein monomer
amino acid
protein polymer
polypeptide (protein) e.g. haemoglobin
nucleic acid chemical elements
carbon, hydrogen, oxygen, nitrogen, phosphorus
nucleic acid monomer
nucleotide
nucleic acid polymer
DNA or RNA
lipids chemical elements
carbon, hydrogen, oxygen
lipids polymer?
NOT A POLYMER
calcium chemical symbol
Ca 2+
sodium chemical symbol
Na +
potassium chemical symbol
K +
hydrogen chemical symbol
H +
ammonium chemical symbol
NH4 +
nitrate chemical symbol
NO3 -
hydrogen carbonate chemical symbol
HCO3 -
chloride chemical symbol
Cl-
phosphate chemical symbol
PO4 3-
hydroxide chemical symbol
OH-
hydrogen functions
regulation of blood pH, involved in transport of CO2
involved in ATP formation in photosynthesis and respiration
ammonium functions
needed for production of nitrates by nitrifying bacteria
production in deamination of amino acids
calcium functions
nerve transmission and muscle contraction
cofactor in blood clotting (prothrombin to thrombin)
bone formation
sodium functions
nerve transmission
affects reabsorption of water in kidney
potassium functions
nerve transmission
in guard cells as part of opening mechanism in stomata
nitrate functions
absorbed by root hair cells
used as source of nitrogen in plants to make amino acids
phosphate functions
bone formation, component of phospholipids
component of ATP and nucleic acids
hydrogen carbonate functions
regulation of blood PH
involved in transport of CO2
chloride functions
cofactor for amylase enzyme
chloride shift in RBC
hydroxide function
regulation of blood pH
polar molecule definition
a molecule that has an uneven charge distribution (partial positive and negative charges which do not cancel out)
what type of bonds are between water molecules
hydrogen bonds
what type of bonds are within water molecules
covalent bond
is hydrogen electropositive or electronegative
electropositive
is oxygen electropositive or electronegative
electronegative (bc greater pull on electron)
electropositive symbol
𝛿+
electronegative symbol
𝛿-
properties of water due to hydrogen bonds
liquid at room temp
density changes
solvent for polar molecules
water & non-polar molecules reactions
cohesion & surface tension
high specific heat capacity
high latent heat of vaporisation
water is a reactant
why is water liquid at room temperature?
the hydrogen bonds between H2O molecules make it more difficult for them to escape and become a gas
water is suitable for ‘what’ because it is liquid at room temperature?
provides a habitat e.g. lakes, rivers, seas
be a major component of tissues
be a reactions medium for chemical reactions
be an effective transport medium e.g. blood
explain water’s change in density with temperature
cooling of water allows maximum number of hydrogen bonds to form so water molecules space out to allow this and water expands as it breezes. Therefore ice is less dense than water and floats. This creates currents.
why are water’s changes in density useful
the currents created allow circulation of water.
a layer of ice will float to the top of water and insulate a pond against extreme temperatures, decreasing heat loss so aquatic organisms have a stable environment
ice floats so provides land for terrestrial animals
why is water a good solvent?
water molecules cluster around charged parts of solute molecules or ions and keep them apart bc water is polar
water is useful for ‘what’ because it is a good solvent?
molecules can move around in solvent and react together
molecules and ions can be transported when dissolved
good for removal of water e.g. urea in urine
what happens to non-polar molecules when surrounded by water?
they are pushed together, allowing hydrophobic reactions to occur
what do hydrophobic reactions allow for
tertiary structure of proteins to form
phospholipid bilayer to form
how do the properties of water enable globular proteins to be soluble?
water can form hydrogen bonds with the hydrophilic groups of the amino acids in these proteins
how does cohesion work?
water molecules are attracted together as a result of hydrogen bonds
how does surface tension work?
at the surface of water, water molecules are all hydrogen bonded to the water molecules beneath, giving the surface of the water the ability to resist force applied to it
uses of cohesion and surface tension?
columns of water are pulled up xylem in the transpiration stream
insects e.g. pond skaters can walk on water
jellyfish keep shape in water because molecules not easily compressed so this gives jellyfish support
what is water’s specific heat capacity
HIGH : 4.2 kJ of energy required to raise the temp of 1kg of water by 1C
why does water have a high specific heat capacity
hydrogen bonds restrict movement of water molecules and therefore a large amount of energy is needed to raise the temperature
uses of water’s high specific heat capacity
water does not warm up or cool down easily (high thermal stability)
water keeps a stable temperature, giving aquatic organisms a stable environment in which to live
gases remain soluble in water e.g. oxygen for aerobic respiration of organisms
what is high latent heat of vaporisation
as water molecules are held together by hydrogen bonds, relatively large amounts of heat energy are needed for water to evaporate. this energy helps the molecules to break away form each other
why is water’s high latent heat of vaporisation useful?
helps keep temperature stable
cools organisms e.g. mammals sweating and plants’ perspiration
when is water used as a reactant?
hydrolysis reactions e.g. digestion (catabolic)
raw material of photosynthesis (anabolic)
why is it useful that water is transparent?
aquatic organisms can photosynthesise
what does the wavelength of light do as depth of water increases
it varies
carbohydrates general formula
Cx(H2O)y
types of carbohydrates with short definition and example
monosaccharides= single sugars (short chains or ring) e.g. glucose
disaccharides= double sugars e.g. maltose
polysaccharides=many sugars joined together (branched/unbranched chains) e.g. glycogen
monosaccharides general formula
(CH2O)n n=between 3 and 9
monosaccharides properties
soluble in water because of polar -OH group
insoluble in non-polar solvents
tastes sweet
monosaccharides molecular formula
shows number of each atom
monosaccharides structural formula
shows arrangement of atoms
monosaccharides isomers
molecules with the same molecular formula but different structural formulae e.g. alpha and beta glucose
alpha glucose molecular formula
C6H12O6
alpha glucose functions
energy source
component of (monomer for) glycogen and starch (energy stores)
alpha glucose structure
H on top
beta glucose molecular formula
C6H12O6
beta glucose functions
energy source
component of cellulose (provides structural support to cells)
beta glucose structure
H on bottom
ribose molecular formula
C5H10O5
ribose functions
component of RNA
component of ATP
ribose structure
two OH groups at bottom
deoxyribose molecular formula
C5H10O4
deoxyribose function
component of DNA
deoxyribose structure
OH group bottom left
H bottom right
name of a C=O group
carbonyl group
name of an O-H group
hydroxyl group
name of a H-C=O group
aldehyde group
what is special about a hydroxyl group?
it is polar so makes glucose/ other molecules soluble in water
property of glucose thanks to its polarity? what does this make it useful for
freely soluble in water
therefore soluble in blood plasma and can be transported to cells for uptake
functions of water?
transport
chemical reactions
temperature control
support
movement
reproduction
how is water useful for reproduction?
sexually reproducing organisms sometimes use water to bring gametes together for fertilisation
in mammals the foetus develops in a water-filled sac, which provides physical and thermal stability
bryophytes release antherozoids (male gametes) in moist conditions, which use flagella to swim to oospheres(female reproductive cells) by chemotaxis.
how is water useful for movement?
nastic movements (do not involve growth towards a stimulus) depend on osmotic flow of water e.g. open/close of flowers or the snap of a Venus fly trap
organisms such as earthworms and leeches use hydrostatic skeletons to move around. longitudinal and circular muscles contract against the watery fluid of the coelom
how is water useful for support
plants gain turgidity, which is essential to maintain the maximum surface area, so maximum light is absorbed for maximum photosynthesis and for maintenance of aerial plant parts for increased seed dispersal
water filled tissues contribute to skeletal support. organisms with hydrostatic skeletons need water for the fluid in the coelom against which muscles can act
for aquatic organisms, water provides support through buoyancy and pressure
how is water useful for temperature control
high SHC so water acts as an essential buffer for organisms maintaining a constant body temp for enzyme-controlled reactions to work at optimum temp & regulate metabolism
high latent heat of vaporisation means heat is released when water evaporates, which is a cooling mechanism to keep a stable temp
water remains liquid over a huge temp range, which is essential for metabolism and useful for aquatic organisms which avoid freezing
how is water useful in chemical reactions
combination of thermal stability & solvent properties make water an ideal environment for them reactions. all enzyme reactions of photosynthesis, respiration, excretion e.t.c. occur in solution
when does water act as a reactant
photosynthesis
hydrolytic reactions e.g. digestive enzymes when digesting starch, proteins, lipids
how is water useful for transport in plants
uptake of minerals by plants from soil across root hair cells
transpirations stream
water-based movement of sugars and amino acids in phloem occur in solution
many essential metabolites dissolve completely e.g. glucose, amino acids, vitamins and minerals
larger molecule such as proteins are transported as colloids
transpiration stream held together by cohesion and adhesion (mols bind to side of xylem); these give rise to capillarity in tubes of small diameter
low viscosity so flows easily e.g. in xylem
why are monosaccharides well-suited to their role as an energy source?
large number of carbon-hydrogen bonds
why is water useful for transport in animals?
all transport fluids in animals are water-based e.g. blood plasma and cytoplasm
many essential metabolites dissolve completely e.g. glucose, amino acids, vitamins and minerals
larger molecule such as proteins are transported as colloids
low viscosity so flows easily
how are disaccharides formed
formed by 2 monosaccharides combing together in a condensation reaction, forming a glycosidic bond
disaccharides general formula
C12H22O11 (2 hexoses subtract H2O)
disaccharides properties
taste sweet
soluble in water because of the polar -OH group
some are reducing sugars (donate electrons) e.g. maltose, lactose, cellulose
some are non-reducing sugars e.g. sucrose
disaccharides examples
maltose
sucrose
lactose
cellubiose
is maltose reducing or non-reducing?
reducing
maltose monomers
formed from 2 alpha glucose molecules
maltose function
found in germinating seeds where it is broken down into glucose for respiration
is sucrose reducing or non-reducing?
non-reducing and therefore less reactive
sucrose monomers
alpha glucose and fructose
sucrose functions
how plants transport their sugar in translocation
less reactive as it is a non-reducing sugar
is lactose reducing or non-reducing?
reducing
lactose monomers
beta galactose and alpha glucose
lactose function
sugar found in milk
is cellubiose reducing or non-reducing?
reducing
cellubiose monomers
2 beta glucose molecules
cellubiose function
formed as an intermediate during cellulose production
enzyme for condensation reaction for synthesis of a disaccharide
glycogen synthase
bond formed in condensation reaction for synthesis of a disaccharide
glycosidic
condensation reaction for synthesis of a disaccharide description
2 hydroxyl (-OH) groups line up alongside each other.
one combines with a hydrogen atom of the other to form a water molecule.
this allows an oxygen bridge to form between them
this forms a disaccharide
enzyme for the hydrolysis of a disaccharide
maltase
hydrolysis of a disaccharide description
a water molecule is used to split the disaccharide during digestion by providing a hydroxyl group (-OH) and a hydrogen (H), which help the glycosidic bond to break
reducing agent definition
a chemical species that ‘donates’ an electron to an electron recipient , reducing the recipient.
it is oxidised
oxidising agent definition
a substance that ‘accepts’ or ‘receives’ an electron from a reducing agent, therefore oxidising it.
it is reduced.
in terms of hydrogen, oxygen and electrons, oxidation is….
loss of hydrogen
gain of oxygen
loss of electrons
in terms of hydrogen, oxygen and electrons, reduction is ….
gain of hydrogen
loss of oxygen
gain of electrons
are all monsaccharides and disaccharides reducing sugars?
all monosaccharides are reducing sugars
some disaccharides are reducing sugars
how do you know if a sugar is reducing or non-reducing?
any sugar containing a hemiacetal is a reducing sugar
how can you test for a reducing sugar?
it tests positive with Benedict’s solution (blue to orange/brick red)
which compound does Benedicts reagent contain?
copper (II) sulfate
positive test for Benedicts
an insoluble brick-red precipitate is formed
why is an insoluble brick-red precipitate formed which a reducing sugar and Benedicts?
copper ions are reduced by the sugar by gaining electrons from it
as a result, copper (II) oxide is produced
Cu 2+ gains an electron to become Cu +
reducing sugar is oxidised to form a carboxylic acid
what is a qualitative test?
positive or negative result
tells us if a particular substance is present
what is a quantitative test?
tells us how much (concentration) of a substance is present
what is a semi-quantitative test?
involving less than quantitative accuracy e.g. could have estimated concentration by comparing colour change with the colour change of a known concentration
safety precautions for reducing sugar test
wear eye protection
if you get chemicals in your eyes, flush for 20 minutes with eye wash
wash any chemical off skin
step-by-step how to test for reducing sugar
is it qualitative,quantitative or semmi-quantitative
add 5cm Benedicts reagent and stir with glass rod
heat in water bath at 80C for 9 minutes
positive result= green/yellow/orange/brick-red precipitate
negative= blue
semi-quantitative
how to use commercially manufactures glucose test strips
use?
what are the positive/negative results?
dip strip in solution and compare with calibration card
testing urine of diabetics
pos= shows 1000mg/dl
neg= shows 0mg/dl
how to test for a non-reducing sugar?
carry out a normal reducing sugar test (negative with sucrose, so proves absence of RS)
take sample and boil with 1cm HCl with antibumping granules and point away from yourself
cool solution
add sodium hydrogen carbonate powder to neutralise
carry out reducing sugar test again (positive with sucrose to prove presence of non-RS)
basis of non-reducing sugar test
a disaccharide can be hydrolysed into constituent monosaccharides by boiling with hydrochloric acid
this frees up ‘reducing groups’
e.g. sucrose id hydrolysed into glucose and fructose (both RS)
expected result with RS and NRS tests for glucose, sucrose and a mixture of the two
glucose: positive for both, and the same colour for both
sucrose: negative for RS, positive for NRS
mixture: positive for RS, larger positive result for NRS (if both brick red, w/ no visible difference, filter and measure mass of ppt or use colorimeter on supernatant)
why do you use excess Benedicts in the RS test?
ensures all sugar reacts withe the benedicts reagent
therefore mass of ppt is proportional to conc of glucose, ensuring calibration curve is accurate
why is the reducing sugar content of fruit juice likely to be different from the glucose content?
not all the sugar present in the juice will be glucose
most fruit juice also contain high conc of fructose
fructose will react with the Benedicts to give a greater mass of ppt
therefore when interpolating from the glucose calibration curve, the estimate is for the conc of RS,not an accurate estimate for the conc of glucose
what does a colorimeter measure in a quantitative analysis of the RS test?
how does absorbance relate to glucose conc?
the absorbance of orange light by the supernatant
little glucose present= high absorbance reading (low transmission reading)(very blue, lots of unreacted Cu2SO4)
high conc of glucose= low absorbance reading (high transmission reading)(no colour, little unreacted Cu2SO4)
equation for calculating volume of stock solution required
total volume wanted/ conc of stock solution x conc wanted
controlled variables when using a calibration curve to estimate unknown glucose conc.s
vol. of glucose solution (0.5cm)
vol. of Benedicts(5cm)
temp of WB (80C)
time in WB (9 mins)
type of filter paper(fine grade)
colour of filter in colorimeter (orange or red)
same solution used to 0 colorimeter (distilled water)
precautions when measuring mass of precpitate
avoid spills
stir before filtering (less ppt left in tube)
wash out tube and pour washings through filter
use same quality-fine grade filter paper
record mass of filter paper at start
dry filter paper to constant mass
what is it referred to as when you find the concentration of a substance in a sample by comparing it with known standards
an assay
glycosidic bond definition
a bond formed between 2 monosaccharides by a condensation reaction
polysaccharide defintion
polymers which consist of hundreds/thousands of monosaccharides joined together by condensation reactions, resulting in the formation of glycosidic bonds
homopolysaccharide definition and 4 examples
made up of one type of monosaccharide only
e.g. starch, cellulose, glycogen, callose
heteropolysaccharide definition and an example
made up of more than one type of monosaccharide
e.g. hyaluronic acid
4 properties of polysaccharides which make them good energy stores
hold glucose molecules in chains, so individual molecule can be removed easily
glycogen and starch are compact
glycogen and amylopectin are branched
polysaccharides are insoluble
why is it useful that polysaccharides hold glucose molecules in chains?
individual molecules can be removed in hydrolysis reactions when required so the rest of the chain can remain if not needed
why is it useful that glycogen and starch are compact?
it makes them dense granules so they don’t occupy a large amount of space
why is it useful that glycogen and amylopectin are branched?
they are more compact
offers chance for lots of glucose molecules to be snipped off by hydrolysis at the same time when lots of energy is required quickly
what enzyme breaks 1,4-glycosidic links?
amylase
what enzyme breaks 1,6-glycosidic linkages?
glucosidase
why are polysaccharides insoluble?
they are large macromolecules and the regions which could form hydrogen bonds with the water are hidden away inside the molecule
why is it useful that polysaccharides are insoluble?
they can be stored without dissolving, so will not change the water potential of the cell or affect osmosis
starch monomer
alpha glucose
starch components
amylose
amylopectin
amylose monomer
alpha glucose
what bonds are within amylose
1,4-glycosidic bonds
amylose structure; why?
an amylose helix because a coil is a more compact shape
6 glucose molecules per turn
hydrogen bonds hold helix together
amylopectin monomer
alpha glucose
amylopectin vs amylose : structure
amylopectin is branched and shorter
amylopectin bonds?
1,4-glycosidic bonds in the chains
1,6-glycosidic bonds between chains
amylopectin structure
main chain forms a spiral joined by hydrogen bonds
formation of starch?
amylose helix becomes entangle din amylopectin to form very large starch grains
where are starch grains found?
chloroplasts, seeds and storage organs (e.g. tubers)
where is glycogen found?
animals = liver and muscle cells
fungi
glycogen bonds
1,4-glycosidic bonds in main chain
1,6-glycosidic bonds connecting branches
differences between amylopectin and glycogen
glycogen tend to be even more branches and compact but have shorter 1,4 chains so less tendency to coil
glycogen monomer
alpha glucose
advantage of glycogen having more branches
glucose is released more quickly
cellulose monomer & details
beta glucose
every other beta glucose is rotated 180 degrees
cellulose bonds
1,4-glycosidic bonds between beta glucose molecules
hydrogen bonds between (-OH) groups of molecules
hydrogen bonds between cellulose straight chains which run in parallel to each other
advantage of hydrogen bonds between (-OH) groups of molecules in cellulose
stops the molecule spiralling so they are held in straight chains
advantage of hydrogen bonds between cellulose straight chains which run in parallel to each other in cellulose
increased stability
structure of cellulose fibres
many microfibrils held in bundles by hydrogen bonding make up macrofibrils
cellulose cell wall structure
typically has several layers of fibres running in different directions, giving a high tensile strength
other polysaccharides such as pectins cross link with cellulose fibres to create the cell wall’s glue-like matrix structure
cellulose cell wall 6 properties
very high tensile strength because of glycosidic and hydrogen bonds
can withstand large turgor pressure in cells (due to osmosis) so the cell won’t burst
supports plant (hydrostatic skeleton)
freely permeable (bc of space between macrofibrils) so water and solutes can reach the plasma membrane
insoluble because its a large macromolecule
can be reinforced with other substances to support or waterproof, such as lignin and Suberin
arrangement of macrofibrils determines the growth and change of cell shape e.g. guard cells
why can humans not digest cellulose
humans don’t produce cellulase so cannot break down cellulose
therefore it is the fibre of our food
can ruminants digest cellulose?
yes, ruminants e.g. cows have symbiotic bacteria Ian their stomachs which digest cellulose
elements in lipids
carbon, hydrogen and oxygen
proportion of hydrogen and oxygen in lipids
higher proportion of hydrogen compared to oxygen
types of lipids
most common= triglycerides e.g. fats and oils
derivatives e.g. phospholipids, waxes, steroids (cholesterol)
what are true lipids
esters of fatty acids and alchohol
properties of lipids
insoluble in water, soluble in organic solvents e.g. ethanol
high in energy
why are lipids insoluble in water
because they are non-polar
lipids energy per gram compared to carbohydrates
34kJ/g
carbs= 17kJ/g
why are lipids high in energy
they are rich in C-H bonds
general formula of a fatty acid
R.COOH
what group does a fatty acid contain
carboxyl (carboxylic) acid group -COOH
what is stearic acid an example of; is It saturated/unsaturated and why
example of a fatty acid
saturated because it contains the maximum number of hydrogens and no double C-C bonds
unsaturated fatty acid description and example
fatty acid with one or more carbon double bond, causing a kink in the chain
linoleic acid
polyunsaturated vs monounsaturated
poly= more than 1 carbon double bond
mono= only 1 carbon double bond
do unsaturated fatty acids have higher or lower melting points and why?
double bonds make fatty acids melt more easily (lower MPs) so they are more likely to be liquid at room temperature
examples of saturated and unsaturated lipids
saturated: butter, lard
unsaturated: oils e.g. sunflower oil
how is a triglyceride formed?
by joining a glycerol molecule to 3 fatty acid molecules.
each fatty acid molecule joins via a condensation reaction
type of bond formed between fatty acid and hydroxyl group on glycerol
ester
process of triglyceride formation name
esterification
functions of triglycerides
energy source
energy store
insulation
buoyancy
protection
why are triglycerides useful as energy sources?
ester bonds can be hydrolysed to form glycerol and 3 fatty acids, which can be used in respiration to release more energy than the respiration of sugars
respiration of a lipid produces more water than that of carbohydrates
how do camels use triglycerides as a water source?
they store fat in their humps and respire it to release lots of water
why are triglycerides suitable as energy stores?
insoluble so can be stored without affecting the water potential of cells
high energy density
how much energy do triglycerides yield compared to carbohydrates?
about twice as much
why do triglycerides have a high energy density?
they have a greater proportion of hydrogen atoms compared to carbohydrates
they have lots of C-H bonds
examples of triglycerides used as insulators
heat insulator= whales have blubber (adipose tissue) which decreases heat loss to the surroundings
electrical insulator= fatty myelin sheath around some neurones speeds up conduction of impulses
why are triglycerides used for buoyancy
fat is less dense than water, so it allows aquatic organisms to keep afloat e.g. frogs
where/why are triglycerides used for protection
fat around delicate organs e.g. kidneys acts as a shock absorber
what are waxes & an example
lipid derivatives
e.g. Suberin
what are waxes composed of
large alcohols attached to fatty acids (larger than triglyceride)
where are triglycerides used for waterproofing and why
in the waxy cuticle to prevent water loss
what are phospholipids and what are they made from
lipid derivatives
made from triglycerides
how are phospholipids formed?
a condensation reaction between and OH group on a phosphoric acid molecule (H3PO4) and one of the three -OH groups on the glycerol forms an ester bond
how are phospholipids similar to triglycerides?
one of the fatty acids on a triglyceride is replaced by a phosphate group
amphipathic meaning & nature of phospholipids
phosphate group= polar and hydrophilic bc of -OH group
rest of molecule is non-polar and hydrophobic
what happens when phospholipids are mixed with water
they may form a layer with heads in the water and tails sticking up or may form micelles (heads facing outwards and hydrophobic tails facing inwards)
description of phospholipid membrane and why
phospholipids form a bilayer- tails pointing inwards (hydrophobic so move away from water and interact with each other) and heads pointing outwards ( hydrophilic so move towards water extracellularly and intracellularly)
properties of phospholipid bilayer and why
increased stability because the phospholipids are free to move in the layer but will not flip sides
semi permeable so small and non-polar molecules can move through the tails
which molecules can pass through the phospholipid bilayer
small and non polar molecules (lipid soluble / hydrophobic0 e.g. oxygen, steroid hormones
how does length of phospholipid tails affect fluidity ?
interactions between shorter tails are weaker, maintaining fluidity by making the membrane less rigid
how does the saturation of the phospholipid tails affect fluidity?
unsaturated fatty acid tails have ‘kinks’ so cannot pack as closely together, maintaining fluidity by making the membrane less rigid
what is cholesterol and what does it consist of?
a steroid alcohol (because of hydroxyl group)
consists of 4 carbon based rings
where is cholesterol made in animals
all cells, but mainly in the liver because it is used to synthesise bile
where is cholesterol derivative in plants?
in the membrane
called stigma sterol
amphipathic cholesterol?
its hydroxyl group in hydrophillic and aligns towards the phosphate heads
the remainder of the molecule is hydrophobic and associates with the phospholipid tails
what is cholesterol part of?
the bilayer
cholesterol functions
regulates and maintains fluidity of the membrane
makes up steroid hormones and vitamin d
how does cholesterol maintain and regulate the fluidity of the membrane?
at high temps it stabilises the membrane and raises the melting point
at low temps it intercalates between the phospholipids and prevents clustering
examples of steroid hormones
testosterone, oestrogen, aldosterone, cortisol
are steroid hormones and vitamin d hydrophobic or hydrophillic?
hydrophobic (lipid soluble) so can pass across membranes into cells
protein elements
carbon, hydrogen, oxygen, nitrogen (and sometimes phosphorus and/or sulfur)
what are proteins made up of?
amino acids joined by peptide bonds
what is the sequence of amino acids in a protein determined by?
the sequence of bases in DNA
how many different amino acids occur naturally in proteins?
20
in humans, where do essential and non-essential amino acids come from
essential must come from diet
non-essential can be made
what do plants need in order to make amino acids?
nitrates
functions of proteins
essential component of cell membranes
all enzymes are proteins (specific shape important)
antibodies are proteins
haemoglobin (oxygen-carrying pigment)
collagen
keratin (hair)
form structural component of animals e.g. muscle (actin and myosin)
why are proteins an essential part of cell membranes?
act as carriers and pores for active transport and FD
uses of antibodies?
attack and destroy invading micro-organisms
uses of collagen
adds strength to many tissues including bones and artery walls
the 3 components found in every amino acid which are bonded to the central carbon
amino group NH2
carboxyl group COOH
hydrogen atom H
how do amino acids differ from one another
by the R group
what is the simplest R group and which amino acid is it in?
H
in glycine
what is a zwitterion?
a compound with no overall electric charge, which contains separate parts which are positively and negatively charged
how are amino acids amphoteric and why is this useful?
carboxyl group acts as an acid
amino group acts as a base
means that amino acids can act as buffers
what is a buffer?
a substance that helps to resist large changes in pH
polar R groups on amino acids? examples
OH, C=O or N-H
some are positively charged and some are negatively charged
example of amino acid which has a basic R group
arginine
proton/H+ acceptor e.g. NH2 + -> NH3 +
example of an amino acid with an acidic R group
aspartic acids
proton/H+ donor e.g. COOH -> COO-
what happens when an amino acid is dissolved in water
the amino and carboxyl group can ionise
amino group accepts a hydrogen ion to become NH3 +
carboxyl group donates a hydrogen ion to become COO-
reaction to form a peptide bond? what enzyme is used?
condensation
peptidyl transferase enzymes
what type of bond is a peptide bond
covalent
description of peptide bond formation
one amino acid loses a hydroxyl group from its carboxylic acid group
the other amino acid loses a hydrogen atom from its amino group
the C atom of the first amino acid bonds with the N of the second amino acid
1 O and 2 H atoms removed to form water (condensation)
what is the name of:
2 linked amino acids
many linked amino acids
2=dipeptide
many-polypeptide
where are amino acids linked together in living cells
on ribosomes
how to test for proteins?
biuret test (mixture of sodium hydroxide and copper sulphate)
what is albumen? observation of biurets with albumen
egg white protein
purple layer at the interface. after shaking, uniformly purple
(positive result)
observation of biurets with glucose solution
blue layer at the interface. after shaking uniformly blue
(negative test)
basis of biurets test?
a test for peptide bonds
colour formed by a complex between the nitrogen atoms in the peptide chain and the Cu2+ ions
how many levels of protein structure and organisation are there?
4
but not all proteins have all layers
what shape do all proteins have
a characteristic and specific 3D shape
primary structure of proteins
sequence of amino acids held together by peptide bonds
what can a change in one amino acid in the primary structure of a protein do?
example
completely alter the properties of the protein
e.g. sickle cell anaemia: 1 amino acid substitution in haemoglobin
secondary structure of proteins
folding of amino acid chain into alpha helix or beta pleated sheet du to hydrogen bonding between amino acids.
are hydrogen bonds weak or strong?
weak on their own
many together are strong
tertiary structure of proteins
folding of the secondary structure to a form a precise (specific) 3D shape.
what bonds hold together the tertiary structure of a protein?
ionic, disulphide, hydrogen, hydrophobic/hydrophillic
quaternary structure of proteins
a protein which is made up of 2 or more polypeptide chains.
what bonds hold together the tertiary structure of a protein?
ionic, disulphide, hydrogen , hydrophobic/hydrophillic
structure of an alpha helix
polypeptide chains coil into a helix with 36 amino acids per 10 turns of the helix.
helix is held together by hydrogen bonds
what is a hydrogen bond?
a primarily electrostatic force of attraction between an electropositive atom (with a slight positive charge) e.g. hydorgen and a more electronegative atom (with a slight negative charge) e..g nitrogen or oxygen
beta pleated sheet structure
polypeptide chains fold into a zigzag structure, where one chain folds over on itself, producing a beta pleated sheet.
held together by hydrogen bonds
protein tertiary structure in detail
when alpha coils and beta pleats start to fold, along with the areas of straight chains of amino acids, this forms the tertiary structure.
very specific 3D shape due to bonds between amino acids which lie close to each other.
where do the bonds form in the tertiary structure of a protein?
between different types of R groups
what kind of bonds do negatively charged R groups form in the proteins tertiary structure?
ionic bonds
what kind of bonds do uncharged (polar) R groups form in the proteins tertiary structure?
hydrophilic
interacting with each other or the water in the cytoplasm
what kind of bonds do nonpolar R groups form in the proteins tertiary structure?
hydrophobic
interact with each other away from the water in the cytoplasm
what does the quaternary structure of a protein describe?
how the multiple polypeptides are arranged and held together to make the complete molecule(if it is made up of more than one polypeptide chain)
PROTEINS
disulfide bonds description
where do they form?
strength?
hydrogen (H2) is removed
disulfide bond forms between R groups of cysteine amino acids
very strong covalent bond
PROTEINS
ionic bonds description
where do they form?
strength?
what can they be broken by?
electrostatic attraction between oppositely charged R groups
fairly strong
can be broken by changes in pH
PROTEINS
hydrogen bonds
strength
where do they form?
what are they broken by?
relatively weak, but many form a strong hold
between amine and carbonyl groups
between hydroxyl R groups
between other polar R groups
changes in pH or high temperature can break them
PROTEINS
hydrophobic interactions
some of the amino acids that make up proteins have nonpolar groups and are therefore hydrophobic. these have a strong tendency to associate with one another inside the interior of the folded protein to avoid water molecules
PROTEINS
where do hydrophobic and hydrophilic groups point?
hydrophobic R groups point inwards
hydrophilic R groups point outwards and hydrogen bond with water: this makes proteins soluble
fibrous proteins primary structure
repetitive regular sequence of amino acids
fibrous proteins shape
long parallel polypeptide chains crosslinked (bonded e.g. H bonds) at intervals to form long fibres
helical
fibrous proteins stability
stable structure
are therefore strong and unreactive
fibrous proteins solubility
insoluble
fibrous proteins function
support and structural functions
fibrous proteins examples and where are they found
collagen (found in skin and arteries)
elastin (found in skin, arteries and alveoli)
keratin (found in hair, nails, scales)
globular proteins primary structure
irregular amino acid sequence
globular proteins shape
folded into a spherical shape
globular proteins stability
relatively unstable structure
globular proteins solubility
easily soluble because hydrophilic groups point outwards
globular proteins function
metabolic functions
globular proteins examples and why they are globular
enzymes (must be soluble to function)
some hormones e.g. insulin (must be soluble to function, travels in blood)
haemoglobin (carries oxygen in blood)
myoglobin (stores oxygen in muscle cells)
why can triglycerides not be described as polymers?
not composed of monomers/ repeating subunits
how does the lipid content of mycoprotein differ from food that comes from animals?
higher ratio of unsaturated to saturated fat
less (overall lipid/fat)
less/no saturated fat
more unsaturated fatty acids
haemoglobin:
type of protein
shape
amino acids
bonds
is it conjugated?
quaternary structure?
is it soluble?
does it bind specifically to molecules?
function
found where?
globular
spherical
range of amino acids
hydrogen bonds, hydrophobic interactions
yes; haem group
quaternary structure held together by H bonds and hydrophobic interactions. 4 polypeptide chains
yes, soluble
binds to O2, CO2, CO and H+ (therefore acts as buffer)
transports O2 and CO2 in the blood
in red blood cells
insulin
type of protein
shape
amino acids
bonds
is it conjugated?
quaternary structure?
is it soluble?
does it bind specifically to molecules?
function
found where?
globular
spherical
range of amino acids
hydrogen and disulfide bonds
not conjugated
quaternary structure held together by disulphide bonds. 2 polypeptide chains
yes soluble
binds to receptors on muscles and liver
regulates BGL (decreases it)
produced in pancreas, travels in blood plasma
pepsin
type of protein
shape
amino acids
bonds
is it conjugated?
quaternary structure?
is it soluble?
does it bind specifically to molecules?
function
found where?
globular
spherical
327 amino acids, most of which are acidic so aren’t affected by stomach acid
disulphide and hydrogen bonds
not conjugated
no quaternary structure; only 1 polypeptide chain
yes soluble
protease enzyme breaks down proteins to peptides
stomach
collagen
type of protein
shape
amino acids
bonds
is it conjugated?
is it soluble?
does it bind specifically to molecules?
function
found where?
fibrous
fibre
1000 amino acids-long helices. glycine every 3rd amino acid, repetitive
covalent and hydrogen bonds
not conjugated
insoluble
no
high tensile strength, so prevent artery walls from bursting
artery walls, bones, tendons, skin
keratin
type of protein
shape
amino acids
bonds
is it conjugated?
is it soluble?
does it bind specifically to molecules?
function
found where?
fibrous
fibre
cysteine (disulphide bond)
disulfide and hydrogen bonds
not conjugated
insoluble
no
strong, inflexible and waterproof so acts as barrier
skin, hair, nails, hoofs, scales
elastin
type of protein
shape
amino acids
bonds
is it conjugated?
is it soluble?
does it bind specifically to molecules?
function
found where?
fibrous
fibre
range of amino acids
covalent crosslinks, hydrophobic interactions, hydrogen bonds
not conjugated
insoluble
no
gives strength and elasticity to skin and alveoli because it can stretch and recoil
artery walls, skin, bladder, alveoli
haemoglobin function
transports oxygen from the lungs to respiring cells
haemoglobin location
RBCs; each RBC contains 280 million molecule of Hb
haemoglobin molecule structure: how many and which polypeptide chains
globular, made up of 4 tightly packed polypeptide chains
2 identical alpha globin chains and 2 identical beta globin chains
haemoglobin molecule structure: hydrophobic/philic
hydrophobic R groups face inwards; the interactions hold the molecule in a precise 3D shape
hydrophilic R groups point outwards to maintain solubility
haemoglobin polypeptide chains’ structure
each polypeptide has 8 or 9 sections of a helix
each polypeptide has a haem group, which is permanent but not made of protein (a prosthetic group)
therefore it is a conjugated protein
ham group in haemoglobin
porphyrin (polymorphyin) group. it is a flat structure with an iron ion (Fe 2+) at the centre. this gives its colour
ham group binds reversibly with a molecule of O2
haemoglobin equation
Hb+4(O2)<->Hb(O2)4
haemoglobin+oxygen<->oxyhaemoglobin
from a dark purplish colour to a bright red colour
->oxygen associates with Hb to form Hb(O2)4. (loading)
<- oxyhemoglobin dissociates to form Hb and O2 (unloading)
insulin basic structure
disulphide bonds,
alpha helices
beta pleated sheets
insulin shape
why is this important
has a specific 3D shape, which is important for binding to complementary receptors
how does insulin’s shape relate to its function
(what does it bind to, where, what does this lead to)
insulin binds to a tyrosine kinase receptor on its target cells in the liver and muscles
it has a specific shape that is complementary to the target receptor
this leads to other signalling events within the cells, leading to a decrease in BGL
validity defintion?
an experiment is valid if it is suitably designed to answer the question i.e. variables have been controlled
how does the structure of galactose make it suitable for use as a respiratory substrate?
the bonds contain energy, which is released when they are broken by respiratory enzymes
H/OH groups can form H bonds with water so galactose is soluble and can move within the cell
AVP
why is a covalent bond stronger than a hydrogen bond?
covalent bond involves the sharing of electrons between 2 atoms
H bond= electrostatic attraction between electropositive H atom and an electrongeative atom
what is the significance of an R group in an amino acid?
property of R group gives AA its properties
e.g. determines what bonds it forms and whether it faces in/out
difference between polypeptide and protein?
polypeptide translated at ribosomes= linear sequence of amino acids
protein= more than 1 chain of amino acids with a complex shape
why does keratin in hair contain less disulphide bonds than keratin in nails
flexibility increases with decreasing disulfide bonds
hair is more flexible than nails
how do the shape of globular proteins contribute to the maintenance of life?
signalling molecules e.g. hormones; control body systems by binding to receptors
bind to and carry molecules around the body
AS correct, specific shape for substrate so digest food
3 mechanical functions of collagen in the body
prevents bursting of artery walls by allowing them to withstand high pressure
in tendons, bones, cartilage, connective tissue
how can a colorimeter be used to do a quantitative benedicts test?
colorimeter measures absorbance/transmissioon of light by a coloured slution
more conc solution= more light absorbed/less light transmitted
or compare to data table of known concentration
what are the 2 parts that make up a carboxylic acid?
carboxyl group and hydrocarbon chain
why do oils contain unsaturated triglycerides rather than saturated?
1 or more C=C double bonds
cause kink/bend in tail
cannot pack closely together
cannot form more H bonds
lower MP
2 similarities and 1 difference between phospholipids and sterols
BOTH have dual hydrophobic/philic characteristics
BOTH make up plasma membrane
DIFFERENCE sterols are complex alcohol molecules, phospholipids are lipids
alpha glucose structure
H on top
collagen structure
high proportion of glycine means chains can lie close to each other
crosslinks between molecules are staggered to avoid weak points
collagen properties
provides mechanical strength (high tensile strength) due to covalent bonds liking triple helix molecules together
flexible
insoluble
keratin properties
v strong molecule (lots of disulphide bonds: degree of these determines flexibility)
insoluble
mechanical protection
waterproof (prevents entry of waterborne pollutants)
elastin properties
strong and can stretch and recoil without breaking
insoluble
elastin found where?
why?
alveolar walls: allows them to stretch during inhalation and recoil during exhalation to expel air
differences between amylose and cellulose?
amylose= coiled, cellulose has no coiling
alternate molecules flipped 180 in cellulose but monomers are same orientation in amylose
alpha 1-4 glycosidic bonds in amylose, beta 1-4 glycosidic bonds in cellulose
amylose is granular whereas cellulose is fibrous
H bonds within molecule of amylose, H bonds between adjacent molecules of cellulose
which properties of cellulose make it suitable for forming cell walls?
high tensile strength
H bonds can form between adjacent fibres
why is the ability of water to act as a solvent important for the survival of organisms?
reactions medium (e..g metabolic)
transport medium
ionic compounds separate and dissolve in it
can dilute toxic substances
can take in gases e.g. O2
