Topic 1 - Biological Molecules

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AQA A LEVEL BIOLOGY

TOPIC 1: BIOLOGICAL MOLECULES


NOTES
1.1 Monomers and Polymers – 1.2 Carbohydrates
 A-glucose: hydrogen is above carbon ring
MONOMERS AND POLYMERS  B-glucose: hydrogen is below carbon ring

MONOMER: smaller units from which larger


molecules are made
 E.g., monosaccharides, amino acids,
nucleotides
POLYMER: molecules made from many
monomers joined together TEST FOR REDUCING SUGARS
 E.g., polysaccharides, proteins, DNA/RNA
REDUCING SUGARS: a sugar that can donate
CONDENSATION AND HYDROLYSIS electrons to reduce another chemical compound
CONDENSATION REACTIONS: (e.g. all monosaccharides and some
 Join 2 molecules together disaccharides like maltose/lactose)
 Eliminates a water molecule Reducing sugars are tested using Benedict’s
 Forms a chemical bond reagent:
HYDROLYSIS REACTIONS:  Add 2cm3 of the sample to a test tube (grind
 Separates 2 molecules in water if not in liquid form)
 Requires water molecule  Add an equal volume of Benedict’s reagent
 Breaks a chemical bond  Heat the mixture in a gently boiling water
bath for 5 minutes
SACCHARIDES  If a reducing sugar is present, colour will
change to green, yellow, orange or red
MONOSACCHARIDES: monomer from which depending on concentration of reducing
larger carbohydrates are made sugar present
 E.g., glucose, fructose, galactose
DISACCHARIDES: formed from condensation of
two monosaccharides
 E.g., maltose, sucrose, lactose
 Maltose is formed from two a-glucose
molecules
 Sucrose is formed from glucose and
fructose
 Lactose is formed from glucose and
TEST FOR NON-REDUCING SUGARS
galactose
Other disaccharides such as sucrose are non-
POLYSACCHARIDES: formed from condensation reducing sugars which do not change the colour
of many monosaccharides of Benedict’s reagent when heated with it.
To detect a non-reducing sugar:
 Add 2 cm3 of the sample to a test tube with
the same volume of Benedict’s reagent
 Place the test tube in a gently boiling water
bath for 5 minutes
 If the solution has not changed colour, a
The formation of disaccharides and non-reducing sugar is present
polysaccharides from condensation reactions
 Add another 2cm3 of the same sample to
forms a glycosidic bond between each molecule
2cm3 of hydrochloric acid
STRUCTURE OF GLUCOSE o This will hydrolyse any disaccharides
present into monosaccharides
 Monosaccharide  Slowly add sodium hydrogencarbonate to
 Hexose (6-carbon) sugar neutralise the hydrochloric acid
 Can adopt different isoforms (a- and b- o Benedict’s reagent does NOT work in
glucose) ACIDIC conditions
 Re-test the resulting solution by heating it  The presence of starch is indicated by a
with 2cm3 of Benedict’s reagent in a water blue-black colouration
bath for 5 mins
 If a non-reducing sugar was present, the GLYCOGEN
solution should now turn from blue to STRUCTURE OF GLYCOGEN:
orange-brown  Similar to starch but has shorter chains and
o This is due to the reducing sugars is more highly branched
present upon hydrolysis of the non-  Major carbohydrate storage product of
reducing sugar animals
STRUCTURE RELATED TO FUNCTION:
POLYSACCHARIDES  Insoluble so osmotically inactive
o Does not affect water potential of cells
Polysaccharides are polymers of
 Large and insoluble so cannot leave cells
monosaccharides joined together by glycosidic
 Highly branched gives large surface area for
bonds formed by condensation reaction
enzymes to work on
 They are large and thus insoluble
o Can hydrolyse it into a-glucose for
 Their insolubility makes them suitable for
aerobic respiration
storage
 Compact so can be stored in small spaces
 When hydrolysed, they produce mono-
/disaccharides which can be used in
respiration

STARCH
STRUCTURE OF STARCH:
 Chains of a-glucose monosaccharides linked
by 1,4-glycosidic bonds formed by
condensation reactions CELLULOSE
 Unbranched or branched chains
 Unbranched chains are wound into tight STRUCTURE OF CELLULOSE:
coils that make the molecule very compact  Made up of B-glucose monomers
STRUCTURE RELATED TO FUNCTION:  Forms straight unbranched chains which
 Insoluble so osmotically inactive run parallel to one another
o Does not affect water potential of cells o Allows hydrogen bonds to form cross-
 Helical so compact linkages between adjacent chains
o Can be stored in small spaces  Cellulose chains are grouped together to
 Large so cannot diffuse out of cells form microfibrils which arrange in parallel
 Can be highly branched which gives large groups to form fibres
surface area for enzymes to work on STRUCTURE RELATED TO FUNCTION:
o Enzymes can hydrolyse it into a-glucose  Long, straight, unbranched chains run
for aerobic respiration parallel to each other
 Hydrogen bonds allow formation of cross-
links which provide strength and rigidity to
cell wall
 Prevents cell from bursting as water enters
in by osmosis

TEST FOR STARCH


 Place 2cm3 of the sample into a test tube or
on a spotting tile
 Add two drops of iodine solution and shake
or stir
1.3. Lipids
TYPES OF LIPIDS
Lipids are substances that share the following
features:
 Contain carbon, hydrogen and oxygen
 Proportion of oxygen to carbon and
hydrogen is smaller than in carbohydrates PHOSPHOLIPIDS
 Insoluble in water
 Soluble in organic solvents STRUCTURE AND FEATURES OF PHOSPHOLIPIDS:
The main groups of lipids are triglycerides and  In phospholipids, one of the fatty acids of a
phospholipids. triglyceride is substituted by a phosphate-
containing group
ROLES OF LIPIDS  Phosphate heads are hydrophilic (love
 Source of energy: when oxidised, lipids water) and fatty acid tails are hydrophobic
provide 2x more energy than carbohydrates (hate water)
 Insulation: fat store, prevents heat loss from  In contact with water, phospholipids form a
organism bilayer or micelles
 Protection: stored around delicate organs  They are polar molecules
 Waterproofing: lipids insoluble in water STRUCTURE RELATED TO FUNCTION:
 Phospholipids are polar molecules which
TRIGLYCERIDES means in an aqueous environment, they
form a bilayer within cell-surface
STRUCTURE AND FEATURES OF TRIGLYCERIDES: membranes
 Made up of one molecule of glycerol and 3 o Therefore a hydrophobic barrier is
fatty acids joined by ester bonds formed in formed between the inside and outside of
condensation reactions a cell
 Fatty acids can either be saturated or  The hydrophilic phosphate heads help to
unsaturated hold at the surface of the cell-surface
 Saturated lipids are found in animal fats and membrane
do not contain carbon-carbon double bonds  The structure of a phospholipid allows them
 Unsaturated lipids are found in plants and to form glycolipids by combining with
contain carbon-carbon double bonds carbohydrates within the cell-surface
o This allows the molecule to be able to membrane
bend o These are important in cell recognition
o Unsaturated fats cannot pack together as
tightly due to the double bond and are
therefore liquid at room temperature
STRUCTURE RELATED TO FUNCTION:
 High ratio of energy-storing carbon-
hydrogen bonds to carbon atoms
o Good source of energy EMULSION TEST
 High mass to energy ratio
o More energy can be stored in smaller  Add 2cm3 of the sample to a grease-free
masses test tube and 5cm3 of ethanol
 Shake the tube thoroughly to dissolve any
 High H to O ratio
o Important source of water lipid
 Large so insoluble  If a lipid is present, a cloudy white colour is
o Does not affect water potential of cells observed
 As a control, repeat with water as the
sample – the final solution should remain
clear
1.4.1 Proteins
 A change in a single amino acid will lead to a
STRUCTURE OF AN AMINO ACID change in the protein’s shape and therefore
function
Amino acids are the basic monomer units that
form polypeptides. There are 20 naturally
occurring amino acids in proteins.
Each amino acid has a central carbon atom to
which 4 different chemical groups are attached:
 Amino group (-NH2)
 Carboxyl group (-COOH)
 Hydrogen atom
 R (side) group – variable between each
SECONDARY STRUCTURE
amino acid The secondary structure is the 3D folding of a
polypeptide chain. It can form either alpha
helices or beta pleated sheets.
 The H of the -NH has a slight positive charge
which attracts the slight negative charge on
the O of the -COOH
o As a result weak hydrogen bonds form
between them
 This causes the long polypeptide chain to be
FORMATION OF A PEPTIDE BOND folded into a 3D shape
Two amino acids can join together in a
condensation reaction to form a dipeptide.
The OH from the carboxyl group combines with
the H from the amino group to produce water and
links the two amino acids by a peptide bond.

TERTIARY STRUCTURE
The 3D structure of a protein can be twisted and
folded further to give a specific 3D shape.
This is maintained by multiple different bonds
whose position depend on the primary structure
of the protein.
STRUCTURAL LEVELS OF PROTEINS  Disulfide bonds – fairly strong and not easily
The structure of proteins is determined by the broken
order and number of amino acids, the bonding o Form between two cysteines
present, and the shape of the protein.  Ionic bonds – formed between any carboxyl
and amino group not involved in peptide
PRIMARY STRUCTURE bond formation
o They are weaker than disulfide bonds and
The primary structure is the sequence of amino
are easily broken by changes in pH
acids in a polypeptide chain. Many amino acid
 Hydrogen bonds – numerous but easily
monomers join together in a polymerisation
broken
reaction to form a polypeptide.
 The order of amino acids determines a
proteins ultimate shape and thus function
o Lots of the amino acid glycine helps
close packing
 TERTIARY: chain is twisted into second helix
 QUATERNARY: three of these polypeptide
chains are wound together in a helix

QUATERNARY STRUCTURE
The quaternary structure arises when there is
more than one polypeptide chain.
There can also be prosthetic (non-protein)
groups, such as the iron-containing haem group
in haemoglobin.

TEST FOR PROTEINS


The Biuret test is used to detect the presence of
peptide bonds.
 Add the sample in a test tube and add an
equal volume of sodium hydroxide solution
 Add a few drops of dilute copper sulfate
solution and mix gently
 The presence of peptide bonds and hence a
protein is indicated by a colour change from
blue to purple
 The sample will stay blue if no protein is
present

PROTEIN SHAPE AND FUNCTION


There are two basic types of proteins, whose
roles depend on their molecular shape:
 Fibrous proteins (e.g. collagen) have
structural functions
 Globular proteins (e.g. haemoglobin,
enzymes) have metabolic functions

FIBROUS PROTEINS
Fibrous proteins form long chains which run
parallel to each other. These chains are linked by
cross-bridges which forms stable molecules.
One example of a fibrous protein is collagen:
 PRIMARY: unbranched polypeptide chain
 SECONDARY: polypeptide chain is tightly
wound
1.4.2 Enzyme Action
 The enzyme is flexible and can mould itself
ENZYMES AS CATALYSTS around the substrate
 As the enzyme changes shape, the enzyme
Enzymes are globular proteins that act as
puts a strain on the substrate molecule
catalysts.
 This strain distorts a particular bond or
CATALYSTS: substance that can increase the rate bonds in the substrate
of reaction by providing an alternative reaction  This lowers the activation energy needed to
pathway with a lower activation energy break the bond and starts the reaction
The induced fit model is the most recent and
ENZYME STRUCTURE widely accepted model of enzyme action.
Since enzymes are globular proteins, they have a
specific 3D shape that is the result of their amino
acid sequence.
The active site is a functional region of the
enzyme.
 It is made up of a relatively small number of
amino acids
 It forms a small depression within the
LOCK AND KEY
enzyme molecule The lock and key model proposes that the active
The substrate is the molecule on which the site of the enzyme is completely complementary
enzyme acts on. to the substrate and fits the substrate exactly.
 It fits into the active site and forms the  The active site is a fixed shape and doesn’t
enzyme-substrate complex change
 It is held within the active site by bonds that o It is complementary to one specific
temporarily form between certain amino substrate
acids of the active site and substrate  After a successful collision, an enzyme-
substrate complex forms leading to a
reaction
This model is old and outdated and has been
refuted by the induced fit model.

MODELS OF ENZYME ACTION


There are two models of enzyme action that
describe how substrates fit into active sites to
start a reaction.
 Induced fit model
 Lock and key model

INDUCED FIT MODEL


The induced fit model proposes that the active
site forms as the enzyme and substrate interact.
 Before reacting, the enzyme’s active site is
not completely complementary to substrate
1.4.3 Factors affecting enzyme action
 pH
MEASURING ENZYME-CATALYSED  Enzyme concentration
REACTIONS  Substrate concentration
 Concentration of competitive and non-
There are two changed most frequently
competitive inhibitors
measured when measuring the progress of an
enzyme-catalysed reaction: EFFECT OF TEMPERATURE
 The formation of products
 Increasing the temperature up to optimum
 The disappearance of substrate
increases the rate of reaction
Generally for both measurements: o Increase in kinetic energy
 At first, there is a lot of substrate so many o More successful collisions and formation
substrate molecules can come into contact of ES complexes
with the empty active sites  Increasing the temperature above the
 Therefore all enzyme active sites are filled optimum decreases the rate of reaction
at any given moment so the substrate is o As temperature increases, hydrogen and
rapidly broken down into product ionic bonds in the active site begin to
 The amount of substrate decreases as it is break
broken down, resulting in an increase in the o Change in tertiary structure leads to
amount of product denaturation
 As the reaction proceeds, it becomes more  Rate of reaction is 0 when all enzymes have
difficult for substrate molecules to come denatured
into contact with active sites as there are
fewer substrate molecules and more
product molecules which block them from
reaching the active site
 Therefore, it takes longer for the substrate
to be broken down so its rate of
disappearance slows and the rate of product
formation also slows
 The graph eventually flattens out as the
substrate has been used up
EFFECT OF pH
 Enzymes have optimum pH where rate of
reaction is highest
 At pH above and below optimum pH, rate of
reaction decreases
o Change in pH alters charges on amino
acids of the active site, substrate cannot
attach to active site
o Causes hydrogen and ionic bonds in
active site to break
o Change in tertiary structure leads to
denaturation
 Substrate cannot bind to active site and form
ES complex
 Fewer ES collisions and formation of ES
FACTORS AFFECTING RATE OF ENZYME- complexes
o Not enough substrate to fill active sites
CONTROLLED REACTION so further addition of enzyme molecules
The following factors affect the rate of enzyme- has no effect on rate
controlled reactions:
 Temperature
COMPETITIVE INHIBITORS
Competitive inhibitors decrease the rate of
reaction
 They have a similar shape to the substrate
 Blocks/competes with substrate for active
site so substrate cannot bind
 Fewer ES complexes can form
Increasing the concentration of substrate can
EFFECT OF ENZYME CONCENTRATION reduce the effect of the competitive inhibitor
 Competitive inhibition is reversible so
 Increasing enzyme concentration increases
substrate is able to bind at higher
rate of reaction
concentrations
o More active sites available to form ES
complexes to increase rate of reaction NON-COMPETITIVE INHIBITORS
 When enzyme concentration exceeds
substrate concentration, rate of reaction Non-competitive inhibitors also decrease the
plateaus rate of reaction but are irreversible.
o Not enough substrate to fill active sites  Non-competitive inhibitors bind to a site
so further addition of enzyme molecules away from the active site – allosteric site
has no effect on rate  This changes the tertiary structure and thus
the active site of the enzyme
 Substrate is no longer able to bind to the
active site so fewer ES complexes form
 Increasing substrate concentration has no
effect on the rate of reaction as the active
site is permanently changed

EFFECT OF SUBSTRATE CONCENTRATION


 Increasing substrate concentration
increases rate of reaction
o More substrate molecules available to
occupy active sites
o More successful ES collision and
formation of ES complexes
 When substrate concentrations exceeds
enzyme concentration, rate of reaction
plateaus
o All active sites are saturated as there is
excess substrate so not enough active
sites available to increase rate
1.5.1 Nucleic acids: Structure of RNA and DNA
BASE PAIRING
NUCLEOTIDE STRUCTURE
In DNA, the two strands are held together by
Individual nucleotides are made up of three
hydrogen bonds between complementary bases:
components:
 Adenine is complementary to thymine
 A pentose sugar
 Guanine is complementary to cytosine
 A phosphate group
The quantities of adenine and thymine are always
 A nitrogenous base
the same, as well as the quantities of cytosine
o Cytosine, adenine, guanine, thymine or
and guanine.
uracil
However, the ratio of adenine and thymine to
These components are joined by condensation
cytosine and guanine varies between species.
reactions to form a mononucleotide.
 Two mononucleotides can be joined in a RNA VS DNA
condensation reaction by a phosphodiester
Similarities:
bond to form a dinucleotide
 Continuous linking of these mononucleotides  Both RNA and DNA nucleotides contain a
forms a polynucleotide pentose sugar, nitrogenous base and
phosphate
 Both RNA and DNA nucleotides are joined by
condensation reactions to form
phosphodiester bonds
 Both nucleotides posses four nitrogenous
bases
Differences:
 DNA nucleotides have deoxyribose sugar,
whereas RNA nucleotides have ribose sugar
 DNA nucleotides can have thymine, whereas
RNA STRUCTURE RNA nucleotides have uracil instead
RNA is a polymer made up of ribonucleotides.  DNA molecules are double stranded,
 It has a singular relatively short chain whereas RNA molecules are single stranded
 The pentose sugar is always ribose  DNA is longer whereas RNA is shorter
 Includes cytosine, guanine, adenine and
uracil STRUCTURE RELATED TO FUNCTION
tRNA transfers genetic information from DNA to
DNA is double stranded
the ribosomes.
 Both strands can act as template for semi-
rRNA makes up ribosomes, alongside other
conservative replication
proteins.
Weak hydrogen bonds between bases
mRNA is involved in protein synthesis.
 Can easily be broken for replication and
protein synthesis
DNA STRUCTURE Many hydrogen bonds between bases
DNA is a polymer made up of  Provides stability to DNA
deoxyribonucleotides. Double helix with sugar phosphate backbone
 Protects from outside chemical and physical
 It is made up of two long strands of
forces
nucleotides
Double helix
o These strands are joined by hydrogen
 DNA is coiled and compact
bonds between complementary bases
Base pairing
o These strands are antiparallel and twist
 Leads to DNA being able to replicate and
into a double helix
transfer information as mRNA
 The pentose sugar is always deoxyribose
 It contains adenine, thymine, cytosine and
guanine
1.5.2 Nucleic acids: DNA replication
suspended in a solution in separate tubes
SEMI-CONSERVATIVE REPLICATION and spun in a centrifuge

For semi-conservative replication to take place


there are four requirements:
 The four types of nucleotide, each with their
bases
 Both strands of the DNA molecule act as a
template for the attachment of these
nucleotides
 DNA polymerase
 A source of chemical energy is required to
drive the process
The process of semi-conservative replication is
as follows:
 DNA helicase breaks the hydrogen bonds
linking the base pairs of DNA
 Double helix separates into its two strands
and unwinds
 Each strand acts as a template to which
complementary free nucleotides binds by Before DNA replication:
complementary base pairing  DNA of bacteria contained only N15 so had
 Nucleotides are then joined in a two heavy (original) strands
condensation reaction by DNA polymerase After 1 round of DNA replication:
to form a new DNA molecule  DNA of bacteria grown originally in N15
 New DNA molecule contains half the original nutrient solution was then transferred for
DNA – semi-conservative replication one division to a solution containing N14
o DNA molecules contained 1 heavy
DNA POLYMERASE (original) and 1 light strand
DNA polymerase has a specific shaped active After 2 rounds of DNA replication:
site which only binds to a complementary  Another division of 1 heavy and 1 light
substrate stranded DNA
 DNA polymerase can only bind to and add o 50% of DNA molecules contain 1 heavy
nucleotides at the phosphate (3’) end (original) and 1 light strand, 50% contain
 It works from 5’ to 3’ both light strands

EVIDENCE FOR SEMI-CONSERVATIVE


REPLICATION
Meselson and Stahl conducted an experiment to
show that DNA replication is semi-conservative:
 Bacteria were grown in a nutrient solution
containing heavy nitrogen (N15) for several
generations
o N15 was able to be incorporated into the
bacterial DNA bases
 They were then transferred to a nutrient
solution containing light nitrogen (N14) and
allowed to grown and divide twice
 During this process, DNA from different
samples of bacteria was extracted,
1.6 ATP
STRUCTURE OF ATP PROPERTIES OF ATP
ATP is a phosphorylated macromolecule which ATP cannot be stored – it is an immediate source
contains: of energy
 Adenine – nitrogenous base  The low activation energy of the phosphate
 Ribose – 5-carbon sugar that acts as a bonds means they are unstable and thus
backbone release energy immediately
 Phosphates – chain of three phosphate As such, ATP is a better immediate source of
groups energy than glucose as:
 Each ATP molecule releases less energy
than each glucose molecule
o It releases energy in smaller more
manageable quantities
 The hydrolysis of ATP to ADP is a one-step
reaction that releases immediate energy
o Glucose breakdown is a series of steps
HOW DOES ATP STORE ENERGY which releases energy slower

ATP HYDROLYSIS ROLES OF ATP


The three phosphate groups are key as to how ATP is used in energy-requiring processes in
ATP stores energy. cells including:
 Metabolic processes
 The bonds between each phosphate group is
unstable so have a low activation energy o ATP provides the energy needed to build
o This means they are easily broken up macromolecules from their basic
units
 When these bonds break, they release a
considerable amount of energy  Movement
ATP hydrolysis is catalysed by ATP hydrolase o ATP provides the energy for muscle
ATP  ADP + Pi contraction
 Active transport
ATP CONDENSATION o ATP provides energy to change the shape
of carrier proteins in plasma membranes
The conversion of ATP to ADP is a reversible
o This allows molecules or ions to be
reaction, but requires the addition of an inorganic
moved against a concentration gradient
phosphate to ADP to reform ATP:
 Secretion
ADP + Pi  ATP o ATP is needed to form the lysosomes
This is catalysed by ATP synthase. necessary for the secretion of cell
The addition of a phosphate to ADP to reform ATP products
can occur in three ways:  Activation of molecules.
 Photophosphorylation o The inorganic phosphate released during
 Oxidative phosphorylation the hydrolysis of ATP can be used to
 Substrate-level phosphorylation phosphorylate other compounds
o This makes them more reactive, thus
lowering the activation energy in
enzyme-catalysed reactions
1.7 Water and Inorganic ions
SOLVENT
HYDROGEN BONDING
Water is polar so many hydrogen bonds form
Water is a polar molecule between water molecules.
 Oxygen atom has a partial negative charge  This means it can separate ionic compounds
 Hydrogen atom has a partial positive charge since the positive ions are attracted to the
Partial negative charge on oxygen attracts partially negative oxygen and the negative
slightly positive charge on hydrogen of other ions are attracted to the partially positive
water molecules. hydrogen
This forms hydrogen bonds between the Water can therefore dissolve other substances
hydrogen of one water molecule and the oxygen (e.g. inorganic ions, enzymes, urea etc.)
of another water molecule.  It acts as a medium for metabolic reactions
 It acts as a transport medium (e.g. in xylem)
PROPERTIES OF WATER
METABOLITE
Water has several properties that are important
in biology. Water is also a reactive compound.
 Condensation reactions release water and
HIGH SPECIFIC HEAT CAPACITY forms a chemical bond
Water is polar meaning many hydrogen bonds  Hydrolysis reactions require water to break
form between water molecules. a bond
 This allows water to absorb relatively large
amounts of heat energy before its INORGANIC IONS
temperature changes Inorganic ions occur in solution in the cytoplasm
Therefore, it has a high specific heat capacity. and body fluids of organisms, in high
Water can therefore act as a buffer against concentrations in some and low concentrations
sudden temperature changes in others.
 This helps maintain a stable internal body PHOSPHATE (PO43-):
temperature for organisms, since they are  Structural role in DNA
mostly water o Give stability in the sugar-phosphate
HIGH LATENT HEAT OF VAPORISATION backbone
 Stores energy in ATP
Water is polar so many hydrogen bonds form HYDROGEN (H+):
between water molecules.  Determine the pH of solutions and therefore
 These can absorb a lot of energy before functioning of enzymes
breaking, when water evaporates into a gas. SODIUM (Na+):
Water therefore gives a cooling effect upon  Co-transport mechanism for glucose/amino
evaporation. acids across plasma membranes
 This helps organisms maintain a constant  Involved in generating nerve impulses and
body temperature. muscle contraction
IRON (Fe2+):
COHESION  Component of haemoglobin contained in red
Water is polar so many hydrogen bonds form blood cells
between water molecules.  Transports oxygen around the body – oxygen
 This means water molecules tend to stick temporarily binds to it, so it becomes Fe3+
together
Water therefore has high cohesive forces which
can support columns of water (e.g. in xylem) and
provides surface tension at the water-air
boundary

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