Endothermic but happens spontaneously

• high degree of disorder
• delta S is positive so that T delta S >delta H
• outweigh
  

Calorimeter

Source of error:

1. heat capacity of the calorimeter being ignored
2. heat loss due to conduction, convection and radiation
3. thermometer not precise enough
4. specific heat of the solution is assumed to be water but in fact is not

Improvement:

1. determine the geat capacity of the calorimeter and take it into account during calculation
2. provide lagging and lid to the calorimeter, or replace it by a vacuum flask calorimeter
3. for higher accuracy in reading temperature, use a Beckmann thermometer
4. determine the water equivalent of the solution
   

Enthalpy change cannot measure/ find

cannot measure directly:

1. the extent of reaction cannot be controlled
2. side reactions are possible
3. the reaction is slow
4. require high temperature
   

impossible to find:

1. reaction involve many product.
   

Occupy 4s before 3s but remove 4s before 3s orbital

As the shells of electrons get further and further from the nucleus, successive shells become closer in energy. Thus the difference in energy between the second and third shells is less than that between the first and second.

By the time the fourth shell is reached, an overlap between the highest energy orbitals(3d) in the third shell and the lowest energy orbitals(4s) in the fourth shell. Hence electrons fill in the more stable 4s orbitals first, before 3d orbitals are filled. As 4s orbital is at a lower energy level than 3d.

Once the 3d level is occupied by electrons, these repel the 4s electron even further from the nucleus. The 4s electrons are pushed to a higher energy level higher than the 3d level now occupied. Hence, transition metals lose electrons from the 4s level before the 3d level.

Answering difference in ionization enthalpy of Element

1. Increase in number of proton --> effective nuclear charge: increase
   
2. Screening effect of inner shell electron --> : decrease
   
3. Extra stability(write out ground state)
   
4. Electron to electron repulsion --> : decrease
   

進階問題答法(基本問題只涉及以上一項)
同 + 異 + 比較-->outweighing effect

Example: O and N
Oxygen and nitrogen has the same number of electron shell(同), although oxygen has 1 more number of proton than nitrogen(異), the electronic configurations of N and O are [He]2s2 2p3 and [He]2s2 2p4 respectively, where first electron of N being remove is in completely filled 2p3 orbital which give extra-stability . (異)

On the other hand, the first electron of O being removed is in a paired orbital, the electron to electron repulsion will lower its ionization enthalpy.(異)

The extra-stability and electron to electron repulsion together outweigh the effect in increase in proton number.(比較--> outweighing effect) Therefore the ionizationentalpy of N is higher than O

AL Chemistry: Law and definition

Planck's Law:
delta E= hv , Discrete lines of different frequencies must be produced by electrons in the atom undergoing definite, discrete energy changes, as they fall from one specified energy level to a lower one.

Quantization of energy/
Quantum theory of energy:
energy cannot stored by atoms, or other particles in any arbitary quantities, but only come in 'packets' of different sizes of energy, it can only do so in the form of quanta of energy, but not continuously in any arbitary unit.

Series in atomic emission spectrum of hydrogen:
For each series the lines are produced by the electron falling from any of the possible higher energy levels to the same lower, specific energy.

First ionization enthalpy:
The energy required to remove 1 mole valence electrons from 1 mole of neutral atoms in gas phase under standard condition(298 K, 1 atm).

Orbit and Orbital:
Orbit refers to an electron path and has no implication for 3-D distribution in space

Orbital refers to a representation of a region within which there is a probability of finding an electron.

Standard solution:
Solution of known concentration.

---------------------------
Standard enthalpy change of formation:
The enthalpy change when 1 mole of a compound is formed from its constituent elements at their standard state under standard condition.

Standard enthalpy change of combustion:
The enthalpy change when 1 mole of a substances burns completely under standard conditions.

Standard enthalpy change of neutralization:
......when 1 mole of water is formed from neutralization of an acid by a base in dilute aqueous solution......

Hess Law:
The enthalpy change of a reaction is the same whether the reaction takes place in one step or in a series of steps.
Spontaneous reaction:
Reaction of an energetically unstable mixture even if the mixture is kinetically stable. A spontaneous reaction could occur without having to be driven.' Spontaneous' means 'of its own accord' and it does not mean fast.

Entropy:
Measure of the randomness or disorder of a system, e.g. gases are relatively disordered compare to liquid

Free energy change (delta G):
The quantity of chemical energy free to do useful work.

delta G= delta H -T deltaS

-----------------------------------------
Bond enthalpy:
It is an average value of the enthalpy changes for the dissociation of a given type of bond at gaseous state.
Electron affinity:
The enthalpy change involved when 1 mole of gaseous atom acquires an electron.
Lattice enthalpy:
The enthalpy change of formation of 1 mole of the crystal lattice from its constituent ions in the gas phase.

Atomic and ionic radius:
Atomic radius--the effective space occupied by the atom in the direction of its covalent bond. Half of the internuclear distance between bonded atoms in the molecule.

Ionic radius--the effective space occupied by an ion in any direction within a series of ionic
crystals of which the ion is a part.

Bond length:
The internuclear distance between the two bonded atoms measured along the direction of covalent bond.

Electronegativity:
The ability of an atom in a covalent bond to attract the bonding electrons.

Dipole moment:
In a covalent bond when the bonded electron pair is not shared equally between the bonded atoms, this results in the formation of a dipole. This bond is a polar covalent bond. The extent of bond polarization can be measured in terms of a dipole moment, where
q: The formal charge on the bonded atoms
d: The internuclear distance between the bonded atoms.

Coordination number:
The number of nearest neighbor atom/ion in of the same atom/ion.

Hydrogen bond:
It is the interaction of hydrogen atom between two small highly electronegative atoms(N,O,F)
-----------------------------------------------------------
Chemical equilibrium
Dynamic equilibrium:
When the state where the concentrations of all reactants and products remain constant with time, this state is called the equilibrium state. If the equilibrium state is dynamic in nature, that means reactants are converted continually to products, and vice versa. Indeed, the rates of forward and reverse reactions are equal at the dynamic equilibrium.

Le Chatelier's principal

If Change is imposed on a system at equilibrium, the position of equilibrium will shift in the direction that reduces the changes.

Partition coefficient

When solute is added to two immicible layer of solution and then reach equilibrium

Solute(solvent1)<-->solute(solvent2)

partition coefficient= [solute(solvent2)]/[solute(solvent1)]

Paper chromatography

There are a thin film of water which forms a stationary phase on the chromatography paper. The solvent which acts a mobile phase moves up the chromatography paper by capillary action. The amino acids distribute between the stationary and phases. As the three amino acids have different coefficient, they will move up at different rate.

-----------------------------------

Acid base equilibrium

Equilvalence point

The equilvalence pointis the pointat which reactants ave just reacted with each other completely.

End point

The end point is the point at whiich the colour change of the indicator was observed.

Explain why a mixture of HCl and KCl does not dunction as a buffer, whereas a mixture of CH3COOH and CH3COONa does.

For the mixture of HCl and NaCl, since HCL is a strong acid, which will completely dissociate to form hydrogen ion. Hence when a little excess acid wa sdded to this system , H+ ion cannot be removed by Cl-

For the other pair.

CH3COOH(aq) + OH- --> CH3COO- +H2O

CH3COO- +H3O+ --> CH3COOH+ H2O

-------------------------------------

Rate of reaction

Rate of reaction

A change in concentration of a reactant or product in a given time interval.

rate = k[reactant]^n

the proportionality constant k is called the rate constant, where n is the overall reaction order.

The order of a chemical reation

An experimentally estabilished quantity, which is equal to the sum of the powers of the concentrations in a mathematical equation and expressing the rate of the reaction in terms of the concentrations of the substances affecting the rate.

Transition state

The transition state is the temporary state of highest potential energy achieved in a reaction step when the reactants form the product or some other intermediates which will eventually lead to the product.

Molecularity of the reaction

The number of species (atom, ion and molecue) actually taking part in a particular step of a chemical reaction.

Elementary process

A reaction step whose rate equation can be written from its molecularity.

Rate determining step

The slowest step in a sequence of reaction steps. This slowest step controls the overall rate of the reaction.

Mechanism

A set of theoretical steps proposed to account for the conversion of reactants into products in a chemical reaction.

Activation energy

The activation enerhy is the minimum energy required by the reacting particles to initiate a reaction between them. If the energy of reactant is greater than activation energy then the reaction take place.

Homogeneous catalyst

Iron(II) ions may be used a sa homogeneous catalyst in the redox reation between S2O8(2-) and I- since all exist in the same aqueous phase.

Heterogeneous catalyst

Iron powder is a heterogeneous catalyst in Haber Process since iron is in solid state and N2, H2 and NH3 are in gaseous phase. The catalyst is in a different phase from both the reactants and products.

Auto catalyst

An autocatalytic reaction is a reaction in which one of the products acts as a catalyst for the reaction itself. For example. the product Mn2+ ion is the catalyst for the following redox reaction

Application of genetic III

Recombinant DNA technology
The principal:
genetic code for protein production is universal, gene inserted into foreign host cell can still express.

Basic steps:

1. locate specific gene/use DNA probe
2. isolate this gene
3. multiply this gene by polymerase chain reaction
4. insert the gene in vector
5. introduce the gene into host cell in which gene express strongly

limii

1.Locating
--DNA probe

• It is a short strand of DNA that carry part of the base sequence of wanted.
• It will attach to the complementary base sequence in the gene.
• It is radioactive or fluorescent to act as marker.

--Reverse transcription

• mRNA act as a template.
• after complementary DNA is formed from mRNA, mRNA is removed and double strand DNA is made by adding enzyme polymerase and DNA nucleotide
• e.g. retrovirus(HIV e.t.c.)

--Artificial DNA synthesis

• human use DNA polymerase to join nucleotides
• useful for small protein which have short base sequence

2.Isolation
Enzyme/detergent break down cell walls and membranes
Cell debris removed by filtering or cetrifugation
Obtained DNA treated with protease to get pure protein

Enzymes:
Restriction endonucleases
--Cut DNA strands
DNA ligase
--join DNA strands

3.Transferring

• sorting
• multiplication
• insertion
• introduction

Sorting:
gel electrophoresis
--fragment move toward anode
--larger the fragment, more slowly they move

Multiplication
polymerase chain reaction
--automated, rapid and efficient

Insertion
Insert gene a vector which is for transporting DNA into host cell
Types of vector:

1. plasmid= circular ring of DNA found in bacteria
   
2. phages= virus
   
3. cosmid= hybrid of phages
   

Most commonly used is plasmid.
It contain gene for antibiotic resistance where restriction endonucleases are used to break the plasmid loop.
Introduction
plasmids re-introduce into bacterial cell= transformation
Antibiotics are used to identify the cell process the desired gene.

Advantage of recombinant DNA tech

1. Product is pure, work more efficient and less likely to be rejected
2. Large quantity, less expansive
3. Flexible process, made as wanted

-------------------------------------------------
Application of genetic engineering

• microorganism used to control pollution
• GM plant
• transgenic animal
• gene therapy
• genetic fingerprinting

Implications of Genetic engineering

• unpredictable ecology consequence
  

Application of genetics II

Procedure of artificial selection:

1. select individual with best character
2. breed them using sexual reproduction
3. best offspring selected and breed again together
4. this is repeated over generations until offspring have all the desired characteristics

Hybrid Vigour
They are individuals that are heterozygous for a number of different gene
They often show greater fitness, e.g. better growth, productive, disease resistant
The reason for it may not clear as gene may affect more than one trait and heterozygotes may benefit from the effects of a number of different interactions

Polyploidy
cell or organism conains three or more times the haploid number
sterile hybrid: odd number of set of chromosome
fertile hybrid: even number

Inbreeding and Outbreeding:
both are selectively controlled reproduction
Inbreeding:
between closely related individual, e.g. between offsprings, parent and child
+To maintain desirable characteristics
-cause reduced fertility and lowered disease resistance as variation reduced
therefore it is not favoured by animal breeders

Outbreeding:
between member of genetically distinct populations, e.g. different strain or different specises
+introduce new and superior phenotype by gene interaction--heterosis, hybrid vigour

Genetic modification
Method

1. increase activity of gene
2. decrease ...
3. transfer gene between same or different species

Purpose(3 is enough)

• increasing the yield
  
• improving nutrient content of foods
• introducing resistance to disease and pests
• making crop plants tolerant to herbicides
• developing tolerance to environmental condition-hazards
• making vaccines
• producing medicines

Cloning
Cloning is the process of producing populations of genetically-identical individuals that occurs in nature when organisms such as bacteria, insects or plants reproduce asexually. Cloning in biotechnology refers to processes used to create copies of DNA fragments (molecular cloning), cells (cell cloning), or organisms.

Cloning by nuclear transfer:
1. Donor cell taken

• it is culture in low nutrient medium
• nutrient deprived cell stop dividing
• active gene switched off and become dormant

2. Unfertilized egg has nucleus removed
3. Cells are fused

• 1st electric pulse
• time delay allow unknown factors in the cytoplasm to activate chromatid

4. Cell division is triggered

• 2nd electric pulse

5. Embryo surgically implanted into the uterus of the surrogated mother

resource from wiki

Application of genetics I

Basically browing water for whom has not bad biology foundation.

Genetic diseases diagnosis:
Amniocentesis
Chorionic villus sampling

Gene therapy
Germ-line gene therapy:

• defective allele is replaced or supplemented in the fertilised egg.
• All cell of the organism will develop normally.
• Long term effect.

Somatic-cell gene therapy:

• target just affected tissues
• Not evident in gamete,no pass in future generation
• Need to repeat periodically

-Example introducing healthy CRTR gene into lung epithelial cell

• use harmless virus(adenovirus) as a vector, to transfer gene into host cell, OR
  
• wrap the gene in lipid molecules(liposome) to enable it to pass through membranes of lung epithelial cells.

Inheritance of character(B)

Polygenic inheritance
A phenotype/trait may be influence and determined by more than one gene in cumulative way.

features:
The gene individually has little effect but addictive effect is significant.
The multiple gene may or may not be on the same homologous chromosome
It is responsible for the inheritance of quantitative traits.

difficulty in distinguishment of ploygenic inheritance:
Many of the polygenic character is strongly influenced by environmental factors.

Types of variation
Discontinuous variation

• distinct phenotype -->organism place in definite catagory
• qualitiative = cannot be measure
• character controlled by single gene --> not affect by enviroment

e.g. tongue rolling ability

Continuous variation

• gradual transition between two extreme
• quantitative = can be measure
• combined effect of polygene and enviroment
• exhibit normal distribution curve
  

e.g. height

Source of biological variation
A. Reshuffling of gene/gene recombination

• random fusion of gamete during fertilization
• crossing over between homologous chromosome
  
• independent assortment of homologous chromosome

B. Mutation

Mutation
Definition:
A sudden change in amount or structure of genetic material in chromosome which involve change in phenotype.(?)

Occurrence:
Spontaneous mutation-->error in replication, gene mutate itself randomly
Induced mutation-->x-ray, mutagenic chemical e.g. mustard gas

Types of mutation:
1. Change in structure
Deletion: a portion of chromosome is lost
Duplication: a portion of base sequence is duplicated
Inversion:...... is inverted
Translocation: a part of a chromosome breaks off and
---------------join another part of non-homologous chromosome
IDDT

Consequence:
Any change or rearrangement of the sequence will produce wrong sequence of amino acid
--> protein --> enzyme,since enzyme is important in controlling metabolic activities-->Alternation is usually harmful.

2. Change in chromosome number
Usually during meiosis.
One pair of chromosomes fail to separate at anaphase, resulting one gamete in extra and one in missing. This is called non-disjunction.

Inheritance of character (A)

Mendal's first law
The alleles of a gene exist in pairs but when gametes are formed, the member of each pair will segregate(separate) and pass into different gametes. Thus each gamete contains only one allele of each gene.

duel with one unlinked pair of allele (monohybrid inheritance)

Mendal's second law
During meiosis, the two alleles of a gene pair segregate independently. Each member of an allelic pair may assort randomly.

duel with two unlinked pair of allele (dihybrid inheritance)

TtRr x TtRr -->
dominant+dominant :dominant+recessive :recessive+dominant :r+r =
9:3:3:1

Test cross
cross one with homozygous recessive

Back cross
Cross one with its parents.

Gene Interaction
A. Incomplete Dominance
No dominance, intermediate character shown
e.g. Red + White = Pink

B. Codominance
Both dominant, both character shown
e.g. Red + White =Partly Red +Partly White

Multiple allele
Character controlled by more than 2 allele forms in the same locus of a given pair of homologous chromosome.
e.g. human ABO blood group.

Sex Linkage
Usually X-linked
rule

1. male can only pass X to daughter
2. female can pass X to both son and daughter

Linkage
Gene located in the same chromosome move as a unit in nuclear division

With four possible character, maximum of 3 combination can be obtained
e.g. (T link r/ t link R + itself) or (T link r/t link R + T link R/ t link r)
Which does not follow mendal's law.

Crossing over
During synapsis, crossing over may occur between adjacent homologous chromatid at chiasmata.
It is a process of exchange of genetic materials between homologous chromosomes which give rise to new combinations.

e.g. (T link R/ t link r) may produce 3 combination instead of 2.

The closer the proximity of genes the stronger the linkage
The farther apart the genes the more frequent the crossing over.

Importance of linkage and crossing over

• Crossing over causes reshuffling of genes which results in new combination. This lead to greater variation.
• Crossing over is a major source of observable genetic variation within population.
• *Crossing over has Evolutionary significance

*It permits rearrangement of the various alleles between members of homologous chromosome pairs. If a new favourable alleles appear on a particular chromosome, and here is already another favourable alleles appear on a particular chromosome, and there is already another favourable allele at a different locus on the homologous chromosome, crossing over would produce some chromosomes that carry both favourable alleles. Offspring that receive this combination will be favoured by natural selection and will perpetuate the combination. At the same time, offspring receiving the less favourable combination will be selected against, and the frequency of these alleles in the population will diminish .

• discovery of linkage and crossing over led to the mapping of chromosome which promote the study of structure of gene and chromosome
  

174, 175, 56

Significance of cell division

Mitotic cell division

• Growth
• Repair and replacement of body part
• Regeneration of the lost part of the body
• Asexual reproduction

Meiotic cell division

• Essential process in sexual reproduction
  -It preserve a constant number of chromosomes from generation to generation by restoring haploid condition.
  
• Produce genetic variation
  -Synapsis and crossing over
  -radom separation of homologous chromosome in metaphase I and II( independent assortment)
  

Cell division

Cell cycle:
Interphase
Nuclear division (PMAT)

• Prophase
• Metaphase
• Anaphase
• Telophase

Cytokinesis

Interphase
Longest period(G1, S, G2)

• DNA duplication occur
• chromatid start to condense to form chromosome
• spindle apparatus starts to form

--------------------------------------
Mitosis
Prophase
longest state in nuclear division

• chromosome shorten, thicken and become visible
• centriole move to the opposite and become aster as microtubules(spindle fibre) develop
• nuclear membrane and nucleoli disintegrate and disappear

Metaphase

• Spindle well formed
• chromosome are linked to the spindle at centromere
• they arrange along the equator.

Anaphase

• centromere duplicates
• two members of each pair of chromatids separate and drawn to opposite pole by contraction of spindle fibre
• sister chromatids become daughter chromosome
  

Telophase

• daughter chromosome uncoil, lengthen and revert to the invisible interphase conformaion.
• Nuclear membrane reforms
• nucleoli become apparent
• spindle fibres degenerate and disappear

----------------------------------------------
Meiosis
Meiosis I
Prophase I

1. Early prophase I: shorten, thicken, visible+densly stained granule chromomere appear
2. Mid prohase I: pairing of homologous chromosome =synasis, forming bivalent
3. Late prohase I: (a)tetrad apparent in each bivalent
   -----------------(b)non sister chromatid form cross-shape
   -------------------structure called chiasmata, the process
   -------------------involve recombination of genetic material
   -------------------called crossing over(to be discussed later)

And also other change in prophase of mitosis.

Metaphase I, Anaphase I and Telophase I are similar to that in mitosis except the seperation is done on chromosome instead of sister chromatid.

Cytokinesis
Animal only, proceed to meiosis II imediately in plant

Meiosis II
The process of meiosis II is the same as mitosis except there is no replication of DNA occur( S phase in interphase does not exist)
Interphase-->Prophase II-->......
---------------------------------------------
Cytokinesis
Division of cytoplasm
1. animal cell
Furrow form. It deepens and eventually cleaves the cell into two daughter cell.
Furrow appears at the spindle equator so that two daughter cells will have an equal division of cytoplasm and genetic material.

2. plant cell
Cell plate of pectin form in the equatorial region.
It glows until it reaches the edges of the cell and fused with the cell membrane.
Two adjacent daughter cells form.
Strengthening material is laid down on both sides of the cell plate and the cell plate becomes a layer called middle lamina between two newly formed cell

**Centriole, Aster are absent in plant cell division

Genetics: protein synthesis

1. Transcription of DNA
2. Movement of mRNA from the nucleus to the cytoplasm
3. Amino acid activation
4. Translation of mRNA to make a polypeptide

-----------------------------------------------------
Background information
DNA and RNA

Thymine-------------Uracil
helix-----------------single chain
deoxyribose----------ribose
DNA is much too large to be soluble, or to pass through the pores in the nuclear envelope. DNA stay in the nucleus while mRNA and tRNA are small enough to be soluble and move around the cytoplasm of the cell.

mRNA
Shape

• single polynucleotide strand

Feature

• carries copies of genetic information(base sequence), explained as codon for 1 amino acid to ribosome in cytoplasm
  

Function

• act as a template to determine the sequence of amino acids in translation

tRNA
Shape

• single strand, folded into a 'clover leaf'
  

Feature
---amino acid binding site

• Attach specific amino acid

---mRNA binding site = anticodon

• bind specific codon

Function

• (aa binding site)combine various amino acid molecules present in the cytoplasm
• (anticodon)recognize the correct codons on mRNA molecules
• transfer amino acid to the ribosome
  

rRNA

• component of ribosome
• provides site for assembly of amino acids to make protein

-------------------------------------------------------
Transcription

1. Section of DNA molecule unwound by breaking of the hydrogen bond between base pair. This action occurs due to RNA polymerase
   
2. One strand is the template
3. RNA polymerase move along, complementary ribonucleotide is attracted to the template.
4. With the help of RNA polymerase adjacent complementary ribonucleotides are linked until a mRNA is formed. Energy is needed in this process.

Movement of mRNA
The mRNA strand leaves the nucleus through a nuvlear pore and attaches to a ribosome at rough endoplasmic reticulum in the cytoplasm.

Amino acid activation
Enzyme attach amino acid to their specific tRNA molecue. This needs energy supplied by ATP.
Anticodon, which is complementary to the codon on mRNA, specifies particular protein to be attached.

Translation
Ribosome
---Structure

• Non-membrane bound organelles
• Consist of rRNA and protein molecules

---Function

• Sites of protein synthesis
• Act as a translational machinery which hold the mRNA and tRNA-amino acid complex in position

Process
Translation is the synthesis of polypeptide chain using an mRNA molecule as a template. This occurs at the ribosomes by matching the codons on the mRNA molecule with the anticodons on tRNA molecules.

1. In cytoplasm, rRNA bond to the surface/cleft of ribosome
2. mRNA codon read, tRNA anticodon attached to the codon in ribosome
   
3. Next codon read, ......
4. Peptide bond form for 2 amino acid
5. 1st tRNA released,ribosome move along, next codon read
6. Peptide bonds are continuously formed likewise.
   
7. Process stop when the ribosome reach stop condon
8. Polypeptide chain release
   

Primary structure of the produced polypeptides coil and fold to obtain 3-D structure of protein.
mRNA is broken down to regenerate nucleotide.

Polysome
During translation, a mRNA molecule may associate with a number of ribosomes. Such a chain of ribosomes attaching to an mRNA is called a polysome.
Polysome enables a large number of identical polypeptides to be synthesized on a single mRNA strand at a comparatively short period.

reference and resources form
Simon Chiang, Y.K HO