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Biological molecules
Biochemistry: the branch of science that deals with the studies of chemical and physical
processes that take place in the human body
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The key elements of human body are:
❏ Hydrogen
❏ Nitrogen
❏ Oxygen
❏ Carbon
❏ Phosphorous
❏ Sulfur
❏ Potassium
❏ Magnesium
❏ Calcium
❏ iron
How do atoms join together?
Atoms connect with each other by forming bonds known as covalent bonds
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❏ Carbon can form 4 bonds with other atoms
❏ Nitrogen can form 3 bonds with other atoms
❏ Oxygen atoms can form 2 bonds with other atoms
❏ Hydrogen can form 1 bond with other atoms
Ions: an atom or molecule in which the total number of electrons is not equal to the protons
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But if the atom
gains an electron it has a negative net charge and is called anion
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Ions in a solution are called an electrolyte
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Calcium ions
2
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Potassium ions
4
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Ammonium ions
Nerve impulse transmission, muscle
contraction
Nerve impulse transmission, kidney function
Nerve impulse transmission, stomatal opening
Catalysis of reaction, ph determination
Production of nitrate ions by bacteria
Role of anions
1
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Hydrogen carbonate ions
2
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Phosphate ions
acids and protein formation
Maintenance of the blood ph
Balance positive charge of sodium
and potassium ions in the cells
● Cell membrane formation,
nucleic acid and
ATP formation ,
bone formation
●
●
1
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( in carbohydrates the monomers are the sugars, in proteins the monomers
are the amino acids)
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Oxygen has always a much greater share in 0-H
bond
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● Polar molecules interact as the positive and
negative regions of molecule attract each other and
form hydrogen bonds
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Hydrogen bonds give water high specific heat capacity
Hydrogen bonds give water high latent heat of evaporation
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1
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Small molecules
3
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Liquid at a room temperature ( due to hydrogen bonds between water molecules
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Freezes into ice and becomes less dense( because hydrogen bonds are formed,
the h bonds fix the position of the polar molecules further apart than the average
distance in the liquid state
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Water’s polarity makes it very cohesive
...
7
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This means
they will dissolve
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Carbohydrates
●
Carbohydrates means hydrated carbon
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That's the general
formula of the carbohydrates
...
E
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This solubility is imp because it means that glucose can be
dissolved in the cytosol of cell
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This is called condensation reaction
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(a molecule of water reacts with the glyosidic
bond, breaking it apart
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E
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alpha glucose molecules are joined together by the glyosidic bond to form maltose
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Lactose is a disaccharide formed by joining together of Beta glucose and a galactose
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• Three types of polysaccharide are starch, glycogen, cellulose
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Plants store excess energy as starch and when a plant needs
more glucose the starch is converted into glucose
• Starch is a mixture of two polysaccharides of alpha glucose which are (amylose, amylopectin)
• Amylose :
long unbranched chain of alpha glucose, angles of glycosidic bond, angles of glycosidic bond
give it a coiled structure
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➢ Glycogen :
• Main energy storage material in animals
• Animals store excess glucose in the form of glycogen ( another polysaccharide of alpha
glucose
• Structure is similar to amylopectin but has more side branches coming off it
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• Strong fibres means cellulose provides the structural support to the cells
Lipids:
●
●
●
●
●
They are commonly known as fats and oils, fats are solid at room temperature whereas
oil is liquid at room temperature
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( another e
...
of condensation reaction
●
When triglycerides are broken down the water molecules need to be supplied to reverse
the reaction and it is an example of hydrolysis reaction
Saturated and Unsaturated:
1
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Fatty acid with double bond between the carbon atoms is called unsaturated
3
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The presence of two or more bonds between the carbon atoms makes it polyunsaturated
The presence of double bonds make it bend and so the molecules are not closely packed
together which makes them liquid at room temperature
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Sterols are known as steroid alcohols and they are not fats or oils they have complex structure and
have four carbon atoms ring structure
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Amine and carboxylic acid connected to the central carbon atom
2
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When many amino acids join together the reaction is catalused by the enzymes
4
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Four structures of the proteins:
● Primary structure:
Sequence of the polypeptides in the amino acid chain
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This makes it automatically
coiled into an alpha helix or fold it into beta pleated sheet
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More bonds will form
between the peptides
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it has following bonds
1) Hydrogen- weakest of the bonds formed
2) Ionic bonds- stronger than hydrogen bonds and form between oppositely charged r
groups
3) Disulfide bonds- strongest of the bonds and only form between the r groups that contain
sulfur atoms
● Quaternary structure:
The way the polypeptide chains are assembled together
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● insulin a hormone secreted by the pancreas, helps to regulate the blood glucose level
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It consistts of 2
polypeptide chains which are held together by the disulfide bonds
● Amylase:
an enzyme that will catalyse the breakdown of starch
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Its secondary structure contains alpha and beta
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Known as conjugated proteins ( a protein with non
protein group attached)
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Each of the four
polypeptide has a prosthetic group called haem ( contains iron which binds with oxygen)
Fibrous proteins:
Insoluble and strong, which is due to the high proportion of the amino acids
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Has a large proportion of sulfur containing amino acid cysteine
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The
unpleasant smell produced when hair or skin is burnt is due to the presence of the large
quantities of sulfur
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Elastic fibres are present in the walls of the vessels in
the alveoli of the lungs
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It is a
quaternary protein made from many stretchy molecules called tropoelastin
● Collagen:
Found in the connective tissue in the tendons and ligaments
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It also has flexibility
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Benedicts tests for the sugars:
solution into the test tube with a drop or 2 of benedict and heat it in the watre bath for 5
minutes
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The
higher the concentration of the reducing sugar the more the colour would change
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Non reducing sugars:
add dilute HCL and boil it then you add neuralise with sodium hydrogencarbonate and then
add benedicts and look for the colour precipitate
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Starch test:
add iodnine if it is present the colour would g to navy black
4
...
5
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Colorimetry is used to determine the concentration of the glucose solution:
● Benedicts solution and colorimeter to get a quantitative estimate of how much glucose
there is in the solution
● Colorimeter is a device that measures the strength of the coloured solution by
checking how much light passes through it
...
5
● Do benedicts test on each test tube
● Remove any precipitate or leave for 24 hours
● Use colorimeter to measure the absorbance of benedict solution in test tube
● Use results to make the calibraton curve
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e
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The
enzyme catalyses the oxidation of glucose at the elctrodes, this creates a charge
which is converted into the signal by electrodes
Chromatography :
1
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Add small amount of prepared solvent, glacial ethanoic acid and waer is usually used
for amino acids
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Cover
with lid to stop it from evaporating
3
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When the solvent reached neary top take it out and leave it out to dry
5
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The phosphate group forms a covalent bond with hydroxyl group
...
This form long stru ture as a backbone with
base attached to each sugar
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A pentose sugar in dna is called deoxyribose
Each dna has the same sugar, phosphate group
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● ATP - base adenine, sugar ribose and 3 phosphate groups
● ADP- base adenine, sugar ribose and 2 phosphate groups
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Purifying test for DNA :
1
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Make up a solution of the detergent, salt and distilled water
3
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Slowly dribble some cold ethanol down the test tube and it will form a layer on top
9
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5
...
7
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The temperature of the water bath should stop enzymes in the cells from
working properly and breaking down the DNA
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The complementary base pairs ensure that two
strands are identical to orginal
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The abnormal protein might function better than the normal protein or it
might not work at all
Roles of the enzymes:
1
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Dna polymerase catalyses the formation of phosphodiester bonds between the
nucleotides
Triplet code:
The instructions that DNA carries are contained in a sequence of base along the chain of
nucleotides that make up the strand
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It is
a sequence of 3 bases called a codon
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A section of dna that contains the complete sequence of bases to code for entire protein are
called genes
Non-overlapping, degenerate and universal
1) The genetic code is the sequence of codons in the dna which codes for specific
proteins
2) In genetic code each base triplet is read in sequence, seperating the triplet before and
after
3) The genetic code is also degenerate- there are more possible combination of the
triples than there are amino acids, means some aminoa cids are coded for more than
one base
...
5) The genetic code is also universal-the same specific base triplets code for the same
amino acids in all living things
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Complementary base pairing means that the mRNA strand ends up being a
complementary copy of the DNA template strand
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During translation, amino acids join together to
make polypeptide chain in the following sequence of codons carried by mRNA
1
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A tRNA molecule with an anticodon thats complementary to the start codon on
the mRNA attaches itself to the mRNA by complementary base pairing
3
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Ribosomal RNA in ribosome catalyses formation of peptide bond between the
two amino acids attached to the tRNA molecules
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First RNA molecule will move away leaving its amino acids behind
5
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This process continues producing chain of linked amino acid until there is a stop
codon on the molecule
7
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