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Chapter 2: biological molecules
Biological molecule: biological molecule is a loosely used term for molecules and ions that
are present in organisms

Monomers, polymers and macromolecules:
Macromolecule: is a large biological molecule
-> ​polysaccharide
->​ polypeptide​ (proteins)
-> ​polynucleotides​ (nucleic acids)
Macromolecules -> polymers -> monomers (largest to smallest)
Polymer: is a giant molecule made from many similar repeating subunits joined together in a
chain; the subunits are much smaller and simpler molecules known as monomers
Monomer: is a relatively simple molecule which is used as a basic building block for the
synthesis of a polymer; many monomers are joined together to make a polymer, used by
condensation reactions
...
of carbon atoms in each molecule
- (3C) TRIOSES
- (5C) PENTOSES
- (6C) HEXOSES
- All sugars end with ​-ose
Common hexose = glucose, fructose and galactose
Common pentose = ribose and deoxyribose
Hexose = C​6​H​12​O​6

Ring structures:
-

Pentoses and Hexoses have carbon chains long enough to close in on itself​ and form
a more stable ring
...

Carbon 1 joins to Carbon 5, leaving Carbon 6 out of the ring​
...

α Glucose (alpha): -OH is below the ring
β Glucose (beta): -OH is above the ring
These are called isomers (two forms of the same
chemical)
...


• Acid or enzyme hydrolysis followed by
benedict’s test for non-reducing sugars:
Hydrochloric acid is added to a the sample
being tested in the ratio of 1:2 respectively
and heated in a water bath for approximately
2 minutes
...
After this, benedict's test is
carried out
...

Final unit can be​ several 1000 monosaccharides long,​ forming a macromolecule
...
These components are polysaccharides
that are made from a​ ​glucose molecules and contain a 1,4 glycosidic bonds​
...

Amylose is helical in shape and more compact while amylopectin in branched​
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• Glycogen: a macromolecule that is used for the​ storage of energy is animal cells​ and is
also ​made from α glucose molecules​
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Cellulose:
●
●
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​Structural role ​– Mechanically strong molecule

​Polymer of beta ​β​ glucose​ instead of alpha α
​ ​ glucose
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●

Strong molecule​ -​ Hydrogen bonding​ between different cellulose molecules

●

The hydrogen bonds are​ individually weak, but many can form​ due to large number
of Hydroxyl (-OH) groups

●
●
●
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Around​ 60-70 cellulose molecules tightly crosslink​ to form ​Microfibrils
Microfibrils hydrogen bond together to​ form bundles​ called​ Fibres

Cellulose fibres have ​high tensile strength but are still freely permeable

Found in​ cell wall​ - provide ​support​ for plant and helps it withstand the large
pressures from osmosis

Dipoles and hydrogen bonds:
When atoms are held together by covalent bonds, there share electrons with each other
...

Unsaturated: With double bonds​ - ​do not contain maximum possible amount of
hydrogen​
...
Double bonds make fatty acids and lipids melt
more easily
...
Examples:
Plants lipids - Oils eg olive oil
Saturated: Only single bonds​ -​ maximum possible amount of hydrogen
...

Ester: Chemical produced in
reaction between an acid and
alcohol
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​-COOH- acid reacts with -OHalcohol to form the ester bond -COO-
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Triglycerides:
-

Fats and oils
Most common lipid
Glyceride:​ Ester formed by fatty acid bonding with the alcohol glycerol
Glycerol:​ Alcohol with 3 hydroxyl groups​; each of Glycerol's hydroxyl groups bond
with a fatty acid through condensation
Hydrocarbon 'tail'​ vary in length​ depending on fatty acids used
...
ethanol and chloroform
Hydrocarbon tails are​ non-pola​r (no uneven distribution of electrons) which means
they are​ hydrophobic

Roles of triglycerides:
-

-

Energy reserves:​ Lipids are better for storing energy than carbohydrates
because they have more carbon-hydrogen bonds - Lipids of one mass will yield more
energy on oxidation than the same mass of a carbohydrate
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the desert kangaroo never drinks water but instead relies on this process

Phospholipids:
-

-

Special type of lipid
One of the three fatty acid 'tails' is replaced with a phosphate group
Phosphates are​ polar ​- dissolve in water (​ hydrophilic)
One end of the lipid is soluble in wate​r - The phosphate group is hydrophilic and
makes the head of the phospholipid hydrophilic, but the​ two remaining fatty acid tails
are hydrophobic
...
This
mixture is then placed into a test tube

containing the same amount of water
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Proteins:

(hydroxyl group)

 
(sulfhydryl group)

-

(carboxyl group)

(amino group)

 

(methyl group)

Proteins are an extremely important class of macromolecules
...

Some of the many functions of proteins are as hormones, enzymes, antibodies,
oxygen carrying pigments

Amino acids:
Structure​: Central carbon atom bonded to an amine group and a carboxylic acid group
(-COOH-) and a Hydrogen

●

The​ R group​ is what makes every amino acid
different
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Condensation reaction​ - H20 is removed

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Dipeptide​ -​ Two​ amino acids bonded by a peptide bond

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Polypeptide​ -​ Many​ amino acids linked by a peptide bond
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Ribosomes​ - ​Site​ where amino acids join

together to​ form polypeptides​ - controlled by enzymes
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Peptide bond can be​ broken​ by adding H20 -

hydrolysis​ - ​digestion of protein in stomach and small
intestine

Primary structure:
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Sequence of amino acids in a polypeptide chain

●

Polypeptide can consist of ​several hundred amino acids linked by a peptide bond

●

A​ change in one​ amino acid can ​completely alter the polypeptide properties

Secondary structure:

●
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Structure of a protein molecule due t​o regular coiling/folding of the polypeptide
chain​ of amino acids​ eg
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●
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Easil​y broken ​by​ high temperatures and pH changes

Some proteins/ parts of proteins have​ no regular arrangement ​- depends on ​R
groups ​of amino acids present therefore what​ attractions​ occur

Tertiary structure:
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Compact structure of ​3D coiling of the already-folded chain​(secondary
structure) of the amino acids
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1
...
Ionic bonds - ​Bond between two​ oppositely charged R groups​ (​NH3+ and
COO-​groups)
...

3
...
-NH-, -CO- and -OH-​ groups
4
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Hydrophobic R
groups are​ repelled by the watery environment around them and stick together,
though these bonds are​ weak
...
This is called ​denaturing

Quaternary structure:
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3D​ arrangement of​ two or more polypeptide chains​ or a polypeptide chain and
a non protein molecule

●
●

Forms a ​protein

Bonded by the ​same four bonds​ used in the
tertiary structure

Globular and fibrous proteins:

●
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Proteins whose molecules curl up into a ​'ball' shape
...


●

Most globular proteins are​ soluble - hydrophilic R groups on the outside​ of the
protein, therefore water molecules cluster around them
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keratin and collagen

Haemoglobin - a globular protein:
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Oxygen carrying​ pigment in red blood cells

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Globular protein

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Made of​ four polypeptide chains​ - quaternary structure

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Each chain is known as a ​globin

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Two ​of the haemoglobin chains are called​ ​alpha chains​ and made from

alpha-globin​, while the ​two other ones​ are made from ​beta chains​ and are called
beta-globin​
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Hydrophilic R groups​ on the​ outside​ maintain the haemoglobin's ​solubility
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Sickle cell anemia: Glutamic​ ​(hydrophilic a​mino acid) on the surface beta-chain is
replaced​ with ​Valine​ (​hydrophobic​ amino acid) -​ non-polar R group on the outside

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makes it ​less soluble
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Therefore a complete​ haemoglobin molecule can bind with 4 oxygen molecules (8
oxygen atoms)​ at one time since there are four polypeptide chains
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Oxyhaemoglobin​ - When the iron atoms are combined with oxygen
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Collagen - a fibrous protein:
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Fibrous protein

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Makes up​ 25% of total protein​ in mammals - most common

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Structural ​protein

●

Consists of ​3 polypeptide chains ​wound around each other in the​ shape of a helix
(triple helix)

●

Almost every third amino acid is glycine, the​ smallest amino acid​ - found on the
inside​, allows​ 3 strands to lie closer together and form a tight coil​, since any other
amino acid would be too large
...
​ Covalent bonds form between R groups of amino acids​next to each

others, forming cross-links which​ hold many collagen molecules side by side​ forming
●
●
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the ​fibrils​
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Collagen fibres ​line up according to forces ​they must withstand
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●

Achilles tendon​ can withstand a pulling force of ​300N

Water as a solvent:
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Excellent solvent ( substance that dissolves a solution) for​ ions and polar molecules
(unevenly charged molecules) because of​ water is also a polar molecule​ and is
therefore attracted to ions and polar molecules
...
This allows the​ separate ions or chemicals to move freely and
react with other chemicals
...

Water also ​pushes together non-polar molecules​, such as ​lipids​
...


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Important in​ hydrophobic interactions in protein and membrane structure

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Transport medium

High specific heat capacity:
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To raise the temperature of water or change it to a gas, ​molecules need to gain

energy to move more rapidly​
...

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Allows water to​ store more energy​ for the given temperature
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Water has a high heat capacity because of it's hydrogen bonds
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Temperatures of the water inside living organisms is​ more constant so chemical
reactions can happen at constant rates​ and are less likely to be affected by changes
in outside temperature
...
lakes and oceans) less likely to be affected by air
temperature​, providing more stable environments for aquatic organisms

High latent heat of vaporization:
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Latent heat of vapourisation: ​Measure of ​heat needed to change a liquid to gas​
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Living organisms use this as a cooling mechanism, by producing water droplets we
call ​sweat
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Plants also use this to cool leaves during transpiration
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Below 4C, density of water starts to decrease,

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Ice floats on water, insulating the water underneath it
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lakes) to freeze completely, and
makes it more likely for aquatic life surviving in cold conditions
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Water has ​high ​cohesion because of ​hydrogen bonding​
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This also results in high surface tension at the surface of water

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Small organisms, such as pond skaters, can 'skate' over water without falling in,
providing a good habitat for them

Water as a reagent:

●

Water can take part in some chemical reactions

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Photosynthesis​: Sunlight is used t​o ​separate hydrogen from water​
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making ​glucose
(C6H12O6), which is rich in energy,

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The plant produces ​oxygen as a waste product​, which is then used by​ aerobic
organisms for respiration
...
digestion



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