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A level Ch2 Nucleic acids

AS Chapter 8

Lauren McEwen

on 16 November 2018

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Transcript of A level Ch2 Nucleic acids

Nucleic acids
Chapter 2
* Deoxyribose sugar
* Phosphate group
* Organic base – either a single ring base (cytosine (C) & thymine (T)) or a double ring base (adenine (A) & guanine (G))
Nucleotide structure
2.1 Structure of RNA & DNA
Individual nucleotides are made of 3 components:
sugar (5C atoms)
* A
* A
nitrogen-containing organic base
(C, T, U, A & G)
These are combined by condensation to form a
Two mononucleotides are joined by condensation reaction (between the sugar of one mononucleotide and the phosphate of another) to form a
(joined by a
phosphodiester bond
). Continued linking will form a
DNA structure
Determined by Crick & Watson (with more than a little help from Rosalind Franklin!) Made of 2 strands of nucleotides joined together by H bonds between particular bases
* Adenine always pairs with thymine (2 H bonds)
* Guanine always pairs with cytosine (3 H bonds)
Quantities of A & T are always the same, quantities of G & C are always the same, but the ratio varies from species to species.

Uprights of phosphate & deoxyribose wind round one another to form a double helix. For each complete turn of the helix there are 10 base pairs.
Function of DNA
Approx 3.2 billion base pairs in the DNA of a typical mammalian cell
Adapted to carry out its functions in a number of ways:
* Very stable & can pass from generation to generation without change
* 2 separate strands joined with H bonds allowing them to separate during DNA replication & protein synthesis
* Extremely large molecule carrying an immense amount of info
* Base pairs within the cylinder of the backbone, gives some protection from corruption by outside chemicals and physical forces.
* Base pairing leads to DNA being able to replicate and to transfer info as mRNA
Describe the structure of a nucleotide
Describe the structure of RNA
Describe the structure of DNA
DNA structure
RNA structure
* Phosphate group
* Organic base – either a single ring base (cytosine (C) &
(U)) or a double ring base (adenine (A) & guanine (G))
* mRNA transfers genetic information from DNA to the ribosomes, tRNA is involved in protein synthesis, ribosomes are made up of protein and another type of RNA.

The stability of DNA
DNA is a stable molecule because:
* The phosphodiester backbone protects the more chemically reactive organic bases inside the double helix.
* H bonds link the organic base pairs forming rungs between the phosphodiester uprights. There are 3 H bonds between C&G and 2 between A&T, so the higher the proportion of C&G the more stable the DNA molecule.
* There are other interactive forces between base pairs that hold the molecule together (base stacking)
The strands are
. Nucleotides can only be synthesised 'in vivo' in the 5' to 3' direction, because DNA polymerase can only attach nucleotides to the hydroxyl (OH) group on the 3' C molecule.
2.2 Replication of DNA
Cell division occurs in 2 main stages:
DNA helicase
breaks the H bonds linking the base pairs of DNA.
2. The double helix seperates into 2 strands and unwinds
3. Each exposed strand acts as a template to which complementary nucleotides are attracted.
4. Energy is used to activate these nucleotides.
5. The activated nucleotides are joined together by the enzyme
DNA polymerase
to form the 'missing' polynucleotide strand.
6. Each of the new DNA molecules contains 1 of the original DNA strands (hence semi-conservative)
Nuclear division
(meiotic or mitotic)

Meselsohn Stahl experiment
Based their work on 3 facts:
1. All the bases in DNA contain nitrogen
2. N has 2 forms N14 and the isotope N15 which is heavier
3. Bacteria will incorporate N from their growing medium into any new DNA they make.
conservative model
- original DNA molecule remained intact and a separate daughter copy made from new nucleotides.
semi-conservative model
- original molecules splits into 2 strands each of which replicates its mirror image.
Describe the events which take place during DNA replication
Describe the formation of a new polynucleotide strand
Explain the semi-conservative process of DNA replication
What is energy and why do organisms need it?
How does ATP store energy?
How is ATP synthesised?
What is the role of ATP in biological processes?
What is energy?
'The ability to do work'
* It takes many forms
* It can be changed from 1 form to another
* It cannot be created or destroyed
* It is measured in Joules (J)
Why organisms need energy
* metabolism
* movement
* active transport
* maintenance, repair and division of cells
* production of substances
* maintenance of body temperature
Energy flows through living systems in 3 stages
2. CHEMICAL ENERGY converted into ATP during RESPIRATION
3. ATP used by cells to perform useful work
Synthesis of ATP
The conversion of ATP to ADP is a reversible reaction and therefore energy can be used to add an inorganic phosphate to ADP to re-form ATP. This
reaction is catalysed by the enzyme
ATP synthase
The synthesis of ATP from ADP involves the addition of a phosphate molecule. It occurs in 3 ways:
Oxidative phosphorylation
Substrate-level phosphorylation
takes place in chlorophyll-containing plant cells during photosynthesis.
occurs in the mitochondria of plant & animal cells during the process of electron transport in respiration.
occurs in plant and animal cells when phosphate groups are transferred from donor molecules to ADP to make ATP (e.g. formation of pyruvate at the end of glycolysis)
In both photophosphorylation and oxidative phosphorylation ATP is synthesised using energy released during the transfer of electrons along a chain of electron carrier molecules in either the chloroplasts or the mitochondria.
The instability of ATP's phosphate bonds make it a good energy donor but a poor long term energy store (fats and carbohydrates are far better). Cells do not store large quantities just maintain a few seconds supply.

It is a better
immediate energy source
than glucose because:

1. Each ATP molecule releases less energy than each glucose molecule. The energy for reactions is therefore released in smaller, more manageable quantities.

2. The hydrolysis of ATP to ADP is a single reaction that releases immediate energy. The breakdown of glucose is a long series of reactions and therefore the energy release takes longer.
ATP is the source of energy for:
metabolic processes
- building macromolecules from their basic units.
- providing the energy for muscle contraction
active transport
- provising the energy to change the shape of carrier proteins in plasma membranes.
- needed to form the lysosomes necessary for the secretion of cell products.
activation of molecules
- the inorganic phosphate released during hydrolysis of ATP can be used to phosphorylate other compounds in order to make them more reactive (e.g. phosphorylating glucose at the start of glycolysis).
2.3 Energy & ATP
Structure of ATP
ATP is a phosphorylated macromolecule. It has 3 parts:
* adenine - a nitrogen containing organic base
* ribose - a pentose sugar that acts as the backbone to which the other parts are attached.
* phosphates - a chain of 3 phosphate groups

Roles of ATP
How ATP stores energy
The bonds between the phosphate groups are unstable and so have a
low activation energy
, which means they are easily broken. When they do break they release a considerable amount of energy. Usually in living cells it is only the terminal phosphate that is removed.

This is a
reaction catalysed by the enzyme
ATP hydrolase
ATP cannot be stored and so must be continuously made within the mitochondria (hence why cells with a high energy demand have many large mitochondria)
2.4 Water & its functions
Water may be the most abundant liquid on Earth but it has some very unusual properties due to its dipolar nature and the subsequent H bonding that this allows.
The molecule has no overall charge, but the oxygen atom is slightly negative and the hydrogen atoms slightly positive leading to it being described as
Describe the structure of the water molecule.
State the properties of the water molecule
Explain the importance of the water molecule to living organisms
Describe inorganic ions & their roles.
The positive pole of one water molecule will be attracted to the negative pole of another (forming a H bond). Although each individual bond is weak (about 1/10 as strong as a covalent bond) collectively they cause water molecules to stick together and have unusual properties.
Because the water molecules stick (are
) to each other it takes more energy to separate them and so the boiling point is much higher than it otherwise would be (
water has a high specific heat capacity
). Without the H bonds, water would be a gas at most Earth temperatures and life as we know it would not exist.

A high specific heat capacity also allows water to act as a great
buffer against sudden temperature variations
Water also has a
high latent heat of vapourisation
(energy needed to evaporate 1gram of water). this allows
to be a very effective method of cooling body temperature in mammals.
Waters large cohesive forces allow it to be pulled up through a tube (e.g. xylem vessel). It also means that water droplets will have a surface tension strong enough to support small organisms.
The importance of water to living organisms
Water is the main constituent (up to 98%) of all organisms and is also an important environment for life.
Water in
- used in hydrolysis and produced in condensation reactions.
- many chemical reactions take place in an aqueous medium
- a major raw material in photosynthesis.
Water as a
. Water readily dissolves:
- gases such as oxygen & glucose
- wastes such as ammonia & urea
- inorganic ions & small hydrophillic molecules (e.g. amino acids, monosaccharides & ATP)
- enzymes, who catalyse reactions in solution
Other important features:
allows organisms to cool & control body temperature
not easily compressed
& so provides support (hydrostatic skeleton of an earthworm, turgor pressure in plants)
- allows aquatic organisms to photosynthesise, means light can penetrate the eye & reach the retina.
Inorganic ions
Found in organisms in the cytoplasm of cells, body fluids & as parts of larger molecules. Concentrations range from very high to very low.
ions- found in haemoglobin, important in the transport of oxygen.
ions - form a structural role in DNA & energy storage role in ATP.
ions - important in determining the pH of solutions (& so the functioning of enzymes)
Sodium ions
- important in the transport of glucose & amino acids across plasma membranes.
The first 3min 30sec are particularly relevant
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