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Chapter2:Molecular Biology: Pages (63-130)
Chapter2:Molecular Biology: Pages (63-130)
Biology
Pages (63-130)
2.1 Molecules to metabolism – living organisms control their
composition by a complex web of chemical reactions.
PAGE 63
• Today, molecular biology is focused on explaining the range of living
processes in terms of the chemical substances involved.
• They have different properties and so can be used for different purposes.
• Carbohydrates are characterized by their composition.
• They are composed of carbon, hydrogen and oxygen, with hydrogen and
oxygen in the ratio of two hydrogen atoms to one oxygen, hence the
name carbohydrate
Classifying Carbon Compounds
• Lipids are a broad class of molecules that are:
insoluble in water, including:
*Steroids, *waxes, *fatty acids and *triglycerides.
In common language, triglycerides :
are fats if they are solid at room temperature or oils if they are liquid at
room temperature.
Classifying Carbon Compounds
• Proteins are composed of one or more chains of amino acids.
• All of the amino acids in these chains contain the elements carbon, hydrogen,
oxygen and nitrogen, but two of the twenty amino acids also contain sulphur.
• Nucleic acids are chains of subunits called nucleotides, which contain carbon,
hydrogen, oxygen, nitrogen and phosphorus.
• There are two types of nucleic acid: ribonucleic acid (RNA) and
deoxyribonucleic acid (DNA).
Drawing molecules
What is metabolism ?
Page no 66
• Metabolism is the web of all the enzyme catalysed reactions in a cell
or organism.
• All living organisms carry out large numbers of different chemical
reactions.
• These reactions are catalysed by enzymes.
• Most of them happen in the cytoplasm of cells but some are
extracellular, such as the reactions used to digest food in the small
intestine.
• Metabolism is the sum of all reactions that occur in an organism.
What is
metabolism ?
Page no 66
• Metabolism consists of
pathways by which one type of
molecule is transformed into
another, in a series of small
steps.
• These pathways are mostly
chains of reactions but there are
also some cycles
What is metabolism ?
Page no 66
What is metabolism?
Anabolism :endergonic reactions
page 66
• Adhesive properties :
• Adhesion is the force by which individual molecules cling to surrounding
material and surfaces.
Hydrogen bonds can form between water and other polar molecules, causing
water to stick to them. This is called adhesion.
This property is useful in leaves, where water adheres to cellulose molecules in
cell walls.
If water evaporates from the cell walls and is lost from the leaf via the network
of air spaces, adhesive forces cause water to be drawn out of the nearest xylem
vessel. This keeps the walls moist so they can absorb carbon dioxide needed for
photosynthesis.
Properties of water :
cohesive, adhesive, thermal and solvent properties of water.
Page
• Starch is the major storage carbohydrate of most plants. It is laid down as compact
grains in plastids called leucoplasts.
• Starch is an important energy source in the diet of many animals, too. Its
usefulness lies in the compactness and insolubility of its molecule. Also, it is
readily hydrolysed to form sugar when required.
• We sometimes see ‘soluble starch’ as an ingredient of manufactured foods. Here
the starch molecules have been broken down into short lengths, making them
more easily dissolved.
• We test for starch by adding a solution of iodine in potassium iodide. Iodine
molecules fit neatly into the centre of the starch helix, creating a blue–black colour.
Polysaccharides.
• Starch is made by linking together α-glucose molecules.
• As in cellulose, the links are made by condensation reactions between
the OH groups on carbon atom 1 of one glucose and carbon atom 4 of
the adjacent glucose.
• These OH groups both point downwards, so all the glucose molecules in
starch can be orientated in the same way.
• The consequence of this is that the starch molecule is curved, rather than
straight.
• There are two forms of starch. In amylose the chain of α-glucose
molecules is unbranched and forms a helix. In amylopectin the chain is
branched, so has a more globular shape
Polysaccharides.
Polysaccharides.
• Glycogen
is very similar to the branched form of starch, but there is more branching,
making the molecule more compact.
Glycogen is made by animals and also some fungi.
It is stored in the liver and some muscles in humans.
Glycogen has the same function as starch in plants: it acts as a store of
energy in the form of glucose, in cells where large stores of dissolved
glucose would cause osmotic problems.
https://www.iitianacademy.com/ib-dp-biology-slhl-question-bank/
• Question 1 /paper 2
• Nitrogen is part of many important substances in living organisms.
• Draw labelled diagrams to show a condensation reaction between two amino acids.
Answer Q1 /paper 2
Question 2/paper 2
Lipids/ general characteristics
page 94
1. Contain the elements carbon, hydrogen and oxygen, as do
carbohydrates, but in lipids the proportion of oxygen is much less.
2. are present as animal fats and plant oils, and also as the phospholipids
of cell membranes.
3. Fats and oils their only difference is that at about 20ºC (room
temperature) oils are liquid and fats are solid.
4. Lipids are insoluble in water. In fact, they generally behave as ‘water-
hating’ molecules, a property described as hydrophobic.
5. lipids can be dissolved in organic solvents, such as alcohol (e.g. ethanol)
and propanone (acetone).
Fats and oils are triglycerides.
Page 94
• Fats and oils are compounds called triglycerides.
• A triglyceride is made by combining three fatty acids with one glycerol
• The linkage formed between each fatty acid and the glycerol is an
ester bond.
Fats and oils are triglycerides.
Page 94
Phospholipid:
• A phospholipid has a similar chemical structure
to triglyceride; here, one of the fatty acid groups
is replaced by phosphate .
• This phosphate is ionized and is, therefore, water
soluble.
• So phospholipids combine the hydrophobic
properties of the hydrocarbon tails with
hydrophilic properties of the phosphate.
• Phospholipid molecules form monolayers and
bilayers in water
• A phospholipid bilayer is a major component of
the plasma membrane of cells.
Cholesterol
• The lipid cholesterol is a component of the
diet, particularly when animal fats are
present.
• This lipid, a steroid, is of different chemical
structure from that of the fatty acids.
• The ‘skeleton’ of a steroid is a set of
complex rings of carbon atoms; the bulk of
the molecule is hydrophobic, but the polar
–OH group is hydrophilic.
Fatty acids Page 95
• fatty acids combined in a triglyceride may vary in their
length (hydrocarbon chain ).
2. use of nomogram.
BMI can also be found using a type of chart called a
nomogram. A straight line between the height on the
left hand scale and the mass on the right hand scale
intersects the BMI on the central scale.
BMI
Data –Based Questions:
Nomograms and BMI
Many research has been done to try to identify factors that increase
the risk of CHD. The following factors all increase the statistical risk:
Increasing age
Being male rather than female
Having a family history of CHD
• Shape matters with proteins – their shape is closely related to their function. This is
especially the case in proteins that are enzymes.
• When a protein loses its three-dimensional shape, we say it has been denatured.
• Heat or a small deviation in pH from the optimum can have the effect of
denaturation.
https://youtu.be/hok2hyED9go
• There are many biotechnological uses for proteins
including enzymes for removing stains,
monoclonal antibodies for pregnancy tests or
insulin for treating diabetics.
• Pharmaceutical companies now produce many
different proteins for treating diseases. These tend
to be very expensive, as it is still not easy to
synthesize proteins artificially.
• The Human Genome Project (page 135) has established that the three
million bases of our chromosomes represent far fewer genes than was
originally expected.
• In fact, protein-coding sequences of our DNA account for only
approximately 1.5%. The remainder include some DNA sequences that
regulate the expression of protein-coding genes (regulatory DNA
sequences), but that leaves 70% of our DNA with other roles or none.
(At one time these regions were described as ‘junk’ or ‘nonsense’ DNA’).
Genes and ‘nonsense’
DNA sequences
1. The first step in replication is the ‘unzipping’ of the two strands. An enzyme called helicase unwinds the DNA
double helix at one region, breaks the hydrogen bonds there that hold the strands together and then
temporarily keeps the strands of the helix separated.
• The unpaired nucleotides are now exposed, surrounded by a pool of free-floating nucleotides.
2. In the next step, both strands of DNA act as templates in replication. Complementary nucleotides line up
opposite each base of the exposed strands – adenine pairs with thymine, cytosine with guanine.
3. Hydrogen bonds then form between the complementary bases, holding them in place.
4. Finally, a condensation reaction links the sugar and phosphate groups of adjacent nucleotides, so forming
the new strands.
This reaction is catalysed by an enzyme called DNA polymerase. The enzyme has a ‘proof-reading’ role in
replication, too – any mistakes that start to happen (such as the wrong bases attempting to pair up) are
corrected.
The result is that the two strands formed are identical to the original strands. DNA replication is
DNA replication steps:
DNA replication steps:
The evidence for semi-
conservative DNA replication.
• Experimental evidence that DNA replication is semi-conservative came
from an experiment by Meselson and Stahl.
• In the first step, they grew a culture of the bacterium E. coli in a medium
(food source) where the available nitrogen contained only the heavy
nitrogen isotope, 15N.
• Consequently, the DNA of the bacterium became entirely ‘heavy’.
• These bacteria were then transferred to a medium of the normal (light)
isotope, 14N. New DNA manufactured by the cells was now made of
14N.
• The change in concentration of 15N and 14N in the DNA of succeeding
generations was measured.
• The DNA was extracted from samples of the bacteria from each
succeeding generation and the DNA in each sample was separated.
• This was done by placing the sample on top of a salt solution of
increasing density, in a centrifuge tube.
• Thus, DNA with ‘heavy’ nitrogen ended up nearer the base of the tubes,
whereas DNA with ‘light’ nitrogen stayed near the top of the tubes.
The evidence for semi-
conservative DNA replication.
https://youtu.be/yDQg7uXShUs
Protein synthesis:
https://youtu.be/gG7uCskUOrA
• We have seen that proteins are linear series of amino acids condensed together.
• Most proteins contain several hundred amino acid residues, but all are built from only 20
different amino acids.
• The unique properties of a protein lie in:
1. which amino acids are involved in its construction
2. the sequence in which these amino acids are condensed together.
3. The number of amino acids residues.
The sequence of bases in DNA dictates the order in which specific
amino acids are assembled and combined together.
Protein synthesis:
• All proteins are formed in the cytoplasm, some at free-floating
ribosomes, and others at the ribosomes on RER.
• For this to happen, a mobile copy of the information in the genes has
to be made, and then transported to these sites of protein synthesis.
• That copy is made of RNA and is called messenger RNA (mRNA). It is
formed by a process called transcription.
• So both DNA and RNA have roles in protein synthesis.
What are the main steps in protein synthesis?
• Transcription – the first step in protein synthesis.
• In Stage 2 of protein synthesis, the amino acids of the pool available
for protein synthesis are activated by combining with short lengths of
a different sort of RNA, transfer RNA (tRNA).
• Translation – the last step in protein synthesis