17th Lecture : 21/11/14

Topic : Genetic transfer and recombination

Notes:
1) Genetic recombination refers to the rearrangement of DNA from separate group of genes.
2) Genetic transfer refers to the exchange between2 DNA to form new combinations of genes in a chromosome.
3) Donor cell is the cell that gives a portion of its total DNA and recipient cell that recieved a portion of DNA from donor cell.
4) When the donor's DNA have been incorporated into the recipient's DNA, the resultant cell is called a recombinant.
5) Transformation occurred when gene transfer from one bacterium to another as 'naked' DNA in solution.
6) Griffith's experiment proved the occurring transformation and the hereditary materials as the transforming agent.
A short explanation about Griffth's experiment:
Streptococcus pneumoniae is used in this experiment. Strain S is virulent and has a capsule on it. Strain R is avirulent and has no capsule on it. When live strain R and dead strain S are injected into a mice individually, the mice survived. When live strain S injected into a mice, the mice died. When live strain R + dead strain S injected into a mice, the mice died.
Conclusion: DNA from virulent cell can enter avirulent cell , changing the avirulent strain genetically to make it become virulent.
7) Avery's experiment proved that DNA carried genetic information for transformation but not protein.
A short explanation about Avery's experiment:
Extraction of polysaccharides, lipids, DNA, RNA and protein from strain S pneumococci by chromotography and each of these extraction added individually into strain R. Strain R turns into virulent only when extracted DNA from strain S is added into strain R.
Conclusion: DNA carries genetic information for transformation but not other materials
8) Competence is the alterations in the cell wall that make it permeable to large DNA molecules.
9) Recipient cells have to be competent to take up the donor DNA. Some bacteria are naturlly competent but some undergo treatment to make it competent.
10) Transduction is the transfer of DNA from donor to recipient via a bacteriophage.
11) There are two types of transduction:

• Generalized transduction

- any bacterial genes are transferred
- bacteriophase attack the bacterial host and hydrolysed the bacterial DNA to mix with viral DNA. New protein coat is build up and some bacterial DNA are packaged in a phase caspid. Then the donor lysed release the phase containing bacterial DNA. The phase which contained bacterial DNA is now infect other recipient bacteria cell. Recombination occur, producing a recombinant cell with a genotype different from both the donor and recipient cells.
- The viral DNA is not being transferred in generalized transduction because viral DNA is not integrated into the bacterial genome.

• Specialized Transduction

- specific regions of DNA are transferred
- bacteriophase attack the bacterial host and viral DNA inserted into the bacterial host to integrate into the bacterial genome. The viral genome integrated into the bacterial genome is called prophage. Upon induction, the prophage detaches from the bacterial chromosome. A portion of bacterial DNA remained attach to the detached phase DNA. Therefore, this excised phage infects another bacterium and transfers the bacterium genes from the donor bacterium.
-Only the bacterial gene that close to the site of prophage are transferred.

12) Plasmids are self-replicating covalently closed circular DNA molecules that are usually not essential for survival. There are three types of plasmid:

• Dissimilation plasmid - code for enzymes for catabolism of certain unusual sugars 
• Conjugative plasmid - carries genes for sex pili and transfer of plasmid'
• R factors - carry genes that confer upon their host cell resistance to antibiotics, heavy metals and cellular toxins.

13) Conjugation requires contact between donor and recipient cells. Conjugation required opposite mating type. The donor cell carry plasmid and recipient cell do not caryy plasmid.
14) Gram-negative bacterial cell used pili for contact while gram-positive bacterial cell used sticky surface molecule for contact.
15) There are two types of conjugation transfer:

• Plasmid transfer

-Bacteria that contain F factor (plasmid) are called F+ donor while bacteria that do not contain F factor are called F- recipient.
- Sex pillus is formed between F+ and F- . F factor replicated and transfer to a F-.
- The F- is converted into F+ .

• Chromosome transfer

- Recombination occurred between F factor and chromosome at specific site of each other.
- The insertion of F factor into chromosome results Hfr cell.
- Hfr cell can transfer chromosomal DNA into the F- but F- convert into recombinant F- cell but not F+ cell because only part of the chromosome being transferred.

Activities: No other activity carried out except for teaching...^^

My own explorace:
1) Naked DNA is histone-free DNA that is passed from cell to cell during a gene transfer process called transformation.
2) There are two ways to create competent cells: heat shock and electroporation. Chemically competent cells are created using a series of cold salt washes to disrupt the cell membranes, preparing the cells to accept plasmid DNA. For electrocompetent cells, the cells are chilled and washed with cold deionized water and 10% glycerol.
Heat shock : The plasmid DNA is incubated with host cells to make the plasmid to close contact with the host cells. The plasmid-cell mixture is heated to 45 degree celcius to 50 degree celcius to allow the plasmid DNA enter the bacterial through disrupted membrane. The heated mixture is then placed back in ice to retain the plasmid in the bacteria.
Electroporation: The plasmid-cell misture is exposed to electric current to make pores on the membrane, allowing the entry of plasmid to the host cell.
3) Prophase is the viral genome that integrated into the bacterial genome.
4) Hfr means high frequency recombinant.

Reflection:
Genetic transfer is really a great invention of human. Organisms can change their genotype through genetic transfer. The steps are complicated and genetic transfer may need a long time to make it completely success. However, genetic transfer are not popular in Malaysia because we lacks those technology knowledge and equipment to carry out transfer.

16th Lecture : 21/11/14

Topic: Viruses

Notes:
1) Acellular are not living cells until they invade in living cells.
2) Viruses consist of protein and nucleic acid, viroids consist only RNA, Satellites consist only nucleic acids, while prions consist proteins only.
3) Viruses are the major cause of disease. Viruses are also important members of aquatic world and contribute a lot in evolution.
4) Virion are complete virus particles nand virion consists of more than 1 molecule of DNA or RNA enclosed in coat of protein. They cannot carry reproduce independent of living cells not carry out cell division but still can exist extracellularly.
5) Virion size range is 10-400nm in diameter and most viruses must be viewed with an electron microscope or confocal microscope.
6) The structure of viruses:

• Caspid made up of protein and glycoprotein. They are the protein coat that surrounded nucleic acid. Caspid are formed from a number of individual protein molecules called protomers
• All viruses contain either single or double stranded DNA or RNA but not both.
• The commbination of genome and capsid is called the viral nucleocapsid.
• Some viruses have their capsid covered by envelope. This allow virus to penetrate host cell through membrane fusion.  The envelopes of some viruses are covered by spikes made up of carbohydrates and protein.

7) There are three types of capsids:

• Helical- shaped like hollow tubes with protein walls
• Icosahedral - regular polyhedron with 20 equilateral faces and 12 verticles.
• Complex - do not fit into the category of having helical or icosahedral capsids ( Bacteriophage)

8) A variety of virions have enzymes and some are associated with the envelope or capsid but most are within the caspid.

9) Viral multiplication have common six steps:

    a) Attachment to host cell

- virus have specific receptor attachment

- receptor determines host preference ( maybe more than one host, maybe more than one receptor, maybe specific tissue)

    b) Viral entry

- either the whole virus enter or just the content of the caspid

- There are three methods used : Fusion of viral envelope with host membrane, endocytosis in vesicle and injection of nucleic acid.

    c) Viral uncoating

- If entire caspid enter the host cell, the genetic matrials must be uncoated to make it available for cell's replication.

   d) Synthesis stage

- replication of genetic materials take place, ass well as the production of caspid and tail

- the stage may occur late or early

- ds DNA typical flow

   e) Assembly

- complicated but varies

- some are assembled in nucleus, some assembled in cytoplasm, maybe seen as paracrystalline structures in cell

  f) Virion release

- Viral proteins may attack peptidoglycan or membrane and lyse the host cell

- Enveloped viruses use budding

- viral protein are placed into host membrane

- nucleocaspid may bind to viral proteins

- envelope may derived from host cell membrane, but may be golgi, ER or other

- virus may use host actin tails to propel through host membrane

10) Bacterial and Archaeal Viral infections either undergo virulent phage (one reproductive choice) and temperate phage (two reproductive choices).

11) Virulent phage: Viral DNA multiples immediately upon entry and bacterial host cell will being lysed.

12) Temperate phage : a) reproduce lytically as virulent phages do ( lytic cycle )

                                     b) remain within host cell without destroying it ( lysogenic cycle )

13) A short explanation of lytic cycle:

Phage inject its DNA into bacterial cytoplasm. The bacterial mistakenly replicate viral DNA instead of its own nucleic acid. The viral DNA organise themselves as phage inside the host cell. The host cell lyses and release new phages. The new phage will now infect another host bacterial cells. 

14) A short explanation of lysogenic cycle:

Phage DNA integrated into bacterial chromosome. Prophase DNA is copied during replication of bacterial cells. The bacterial cells that contain prophase DNA will trigger induction and start the lytic cycle. 

15) The advantage of lysogenic cycle to virus are the phage can remain viable but may not replicate and can ensure the survival of host cell for more multiplication of infection.

16) The changes of host with temperate phage are the bacteria become immune to superinfection and phage may express pathogenic toxin or enzyme.

17) The viral infections in eukaryotic cells will results cytocidal infection, cytopathic infection and transformation to malignant cell.

18) There are few types of cancers : tumor, neoplasia, anaplasia and metastasis.

19) Hosts for bacterial and Archael viruses are young, actively growing bacteria. Hosts for Animal viruses are tissue cultures and embryonated eggs. Hosts for Plant viruses are tissue culture or protoplast culture.

Activites :No other activity carried out except for teaching...^^

My own explorace:
1) Virions are physical entities contain nucleocapsid ,capsid and sometime envelop. It exist extracellularly. Viruses are genetic material that occur intracellularly.
2) Superinfection refers to a second infection occurring in a patient having a preexisting infection.
3) Viruses can used as a new source of therapy because bacteriophage able to kill the pathogenic bacteria in body.
4) The largest population of virus can be found in hydrosphere.
5) Cytocidal infectin is an infection that results in cell death either cell lysis.
6) Cytopathic effects are the morphological changes in cell caused by viral infection.
7) Malignant cells are abnormal cells that divide without control and can invade nearby tissues,
8) Benign tumors are the tumors with no cancer cells.
9) Neoplasia is the abnormal new cell growth and reproduction due to loss of regulation.
10) Anaplasia is the reversion to a more primitive or less differentiated state.
11) Metastasis is the spread of cancerous cells throughout body.
12) Apoptosis is a form of cell death in which a programmed sequence of events leads to the elimination of cells without releasing harmful substances into the surrounding area.

Reflection:
I always think that viruses are weird things since they didn't belong to living organisms nor non-living organisms. Their structures are so weird and just like evil aliens. Sometimes I feel like viruses are the things that sent by aliens to destroy our earth because virus had took many people's lives away. 

15th Lecture: 18/11/14

Topic: Mutation

Notes:
1) Mutation is any inheritable change in the base sequence of DNA.
2) Mutant is a strain carrying such a change and different from parental strain. Parental strain also known as wild-type strain.
4) Base substitution is where the mutation happened  when a single base at one point in the DNA sequence is replace with a different base.
5) Base substitutions are divided into silent mutation, missense mutation and nonsense mutation.
6) Missense mutations may lead to significant changes in protein because instead of the original amino acid in the polypeptide chain, a different one is substituted.
7) Silent Mutation almost always occur in the third base of a codon and have no apparent effect. The third base of a codon replaced with another base but the codon is codes for the same amino acid whih results in no change of the protein translated. This happened because genetic code is degenerative.
8) Nonsense mutation is the mutation that forms stop codon. It change from codon codes for an amino acid to codon that codes for a stop codon. The translated protein may or may not be functional depending on degree of shortening.
9) Frameshift mutation include the insertion or deletion of a single base or bases in the DNA sequence.
10) Frameshift mutation will get termination of protein synthesis soon after the mutation because a totally different protein produced from the point of mutation.
11) Spontaneous mutation is a mutation that occurs without a mutagen while induced mutation is a mutation that requires chemical and physical agents to induce a mutation.
12) Spontaneous mutation make errors during DNA replication or just spontaneous alteration of a base.
13) There are four types of mutagens:

• Base analogues

- is a chemical that can substitute for a normal base in DNA sequence
- the common base analog is 5-bromouracil
- 5-bromouracil can substitutes for Thymine, it is most likely to pair with Adenine, however it can spontaneously pair with Guanine.
- In the next DNA replication, the Guanine will pair with Cytosine and this results in the change of one base pair of DNA.

• Chemical Mutagens

- substances what can alter a base that is already incorporated in DNA and change its hydrogen specificity
- chemically alters a base so that a new base pair appears in daughter cells in a later generation.

• Radiation

- Ionizing and nonionizing radiation
- Ionizing radiation have short wavelength, high penetrating power and more powerful. High dose can kill the cell.
- Non-ionizing radiation induce pyrimidine dimers and can kill about 90%-95% of cell. The survivors are normally mutant.

• Intercalating agents 

- planar, 3-ringed molecules whose dimensions are equivalent to purine and pyrimidine.
- may insert during replication between two base pair and pushing them apart.
- It is a frameshift mutation because it results addition or deletion of one or more base pairs.
- Examples: Acridines, Ethidium bromide

14) Mutation rate is the probability that a gene will be mutated in a single generation.
15) Mutation frequency is the frequency at which a specific kind of mutation is found in a population of individuals.
16) There are two ways to identify mutants:

• Positive Selection

-Detection is done by rejecting unwanted parental strain.
-Growing cells in plates containing antibiotics. Only those colonies that able to grow are resistant to antibiotics and we can identify them directly.

• Negative selection

- Negative selection is used to identify mutants that have lost the ability to perform a certain function that their parents had.
-Auxotrophic mutants, for example, are bacteria that have lost the ability to synthesize an essential nutrient.
-The replica-plating technique is used to identify mutants by negative selection.
-Inoculate a histidine enriched medium with bateria. Incubate so that cells can form colonies. This is the master plate.
-Press a sterile velvet surface into the colonies of the master plate. Some cells from each of the colonies adhere to the velvet.
-Prepare two mediums, one with histidine, the other without histidine. Transfer cells from the velvet to each plate.
-Colonies that grow on the histindine enriched medium but not on the medium lacking histidine are His- mutants.
17) Ames test can be carried out to revert mutant to wild type in the presence of a mutagen. Histidine auxotrophs of Salmonella are exposed to an enzymatically carcinogen and reversions to the nonmutant state are selected.

Activites :No other activity carried out except for teaching...^^

My own explorace:
1) Auxotrophy is the inability of an organism to synthesize a particular organic compound required for its growth while prototrophy is characterized by the ability to synthesize all the compounds needed for growth.
2) Nitrous acid causes A-T >< G-C transition. Nitrous acid will deaminates adenine to hypoxanthine, cytosine to uracil, and guanine to xanthine. Hypoxanthine pairs with cytosine rather than with thymine. Uracil pairs with adenine rather than with guanine. Xanthine, like guanine, pairs with cytosine.

Reflection:
Human really can't do anything when facing with mutation. No matter any changes in DNA are unable to cure with any medicines. That's why a lot of patient with genetic disorders are lost of hope because their diseases are unable to cure. The patient's family sometimes also feel so desperate because no much organisation provide help for patients with genetic disorders.

14th Lecture : 14/11/14

Topic: Gene regulation

Notes:
1) There are two modes of gene expression :

• Constitutive expression: Gene is expressed at the same rate all the times
• Inducible expression: Gene expression changes in response to condition

2) There are two major modes of regulation in cell:

 - control the activity of preexisting enzyme

• Post-transcriptional or post-translational - the synthesis of product can be prevented by inhibit the activity of enzyme

 - control the amount of enzyme synthesized

• Transcriptional regulation - the synthesis of product can be prevented by control the level of transcription
• Translation regulation - the synthesis of product can be prevented by control the level of translation

3) The enzyme activity can be regulated by feedback inhibition. Feefback inhibition involves many steps and the end products of the pathway inhibits the activity of the first enzyme. When the end product is used up, the synthesis of product can be resume.

4) Allosteric inhibition is responsible for the end product inhibition because allosteric enzyme has 2 binding sites : active sites and allosteric sites. When the inhibitor(end product) binds to the allosteric sites, the conformation of enzyme changes and substrate no longer binds to the active site. When the concentration of inhibitor(end product) falls, inhibitor dissociates from allosteric site and the active site restores shape.

5) Most bacterial regulation occurs at the transcription level because it would be a waste to make the RNA if neither the RNA notr its encoded protein is needed.

6) There are two types of regulation of transcription: Repression and Induction.

7) To turn "on" or "off" of gene, regulatory protein and environmental sensor are needed. Regulatory protein produces activator or repressor and environmental sensor is small moleccule that activates or inactivates regulatory protein.

8) Enzyme repression inhibit the gene expression and decrease the synthesis of enzyme and it is response to abundance of end-product. Transcription of the operon occur because the repressor is not bind to the operator. When the corepressor binds to the repressor and the repressor binds to the operator, the transciption is blocked. mRNA and proteins it encodes are not made.

9) Enzyme induction turns on the transciption of genes and synthesise the enzyme only when its substrate is present. A repressor binds to the operator and blocks the transciption of the genes. An inducer molecule binds to the repressor and inactivate it. Transcription by RNA polymerase occurs and an mRNA for that operon is formed.

10) Description of trp operon:

trpE, trpD, trpC, trpB, trpA are the structural genes for the tryptophan synthesis. The end product for trp operon is tryptophan. The regulatory gene, trp R will produces mRNA and translate to inactive repressor. When tryptophan is absent, the repressor is inactive and the operon is on. RNA polymerase attached to the promoter and trancribes the operon's genes. When tryptophan is present, it act as corepressor and binds to the repressor to activate the repressor. The operon is off. The activated repressor binds to the operator and blocks the transcription of the operon;s genes. The end product tryptophan itself act as corepressor. Therefore, it is a feedback inhibition which the end product inhibits the activity of the first enzyme.

11) Description of lac operon:

lac Z, lac Y and lac A are the structural genes for lactose synthesis. Lactose are not the preferred carbohydrate source for E.coli. There are CAP site, promoter site and operator site for lac operon. When glucose is present, the lac operon is off even lactose is present because E.coli prefer used glucose as first carbohydrate source. The cAMP level is low and the binding of CAP-cAMP complex to the CAP site is acheived and the RNA-polymerase able to dissociate with the promoter but the active repressor binds to the operator causes the inhibition of transcription. If glucose is absent, the operon is on. The concentration of cAMP increased. The repressor protein binds to allolactose and incapable interact with the operator. CAP-cAMP complex binds to the CAP site and help in the binding of RNA polymerase to the promoter, structural genes are able to transcript and lactose is synthesised. Nevertheless, if glucose is present, the lac operon is repressed even in the presence of lactose. This repression is maintained until the glucose supply is exhausted.

Activities: No other activity carried out in class except for teaching...^^

My own explorace:

1) Too much of tryptophan exist in bacteria is toxic. Therefore, they need to regulate the amount of tryptophan.

2) Cyclic adenosine monophosphate is a second messenger important in many biological processes. cAMP is derived from adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms.

Reflection:

I learnt gene regulation in Form 6 but I learnt new things in this lecture, the cAMP and CAP site. We didn't touch about the cAMP and CAP site for gene regulation chapter in Form 6. The lac operon consists of CAP site and it is for the binding of complex cAMP-CAP. This complex will enhances the dissociation of RNA polymerase to promoter. Everybody felt tired after came back from NUCELL and someone felt sleepy in this lecture but I still concentrate in this lecture because genetic is an interesting topic for me.

13th Lecture : 11/11/14

Topic: Structure and Function of Genetic Material

Notes:
1) Genes are the segment of DNA codes for genetic material.

2) Genome are the genetic information in a cell.

3) Nucleic acid : DNA ( Deoxyribonucleic acid) and RNA ( Ribonucleic acid)

4) Nucleotise is made up of pentose sugar ( ribose and deoxyribose ) , nitrogenous base and phosphoric acid.

5) The structure of Deoxyribose and Ribose:

• The formula for Deoxyribose is C5H10O4 while the formula for ribose is C5H10O5.
• Deoxyribose lack of one oxygen atom.
• Ribose have an OH attach to carbon number 2 instead of H atom.

5) Nitrogenous bases are divided into pyrimidine (Cytosine, Thymine and Uracil ) and purines ( Adenine and Guanine )

6) The structure of nucleotide :

• Nitrogenous base always attach to carbon 1 while phospheric acid attach to carbon 5 and carbon 3 of next pentose sugar.
• Nucleoside composed of pentose sugar and base while nucleotise composed of nucleoside and phospheric acid.
• Polynucleotide is bonded by phosphodiester bond. (between phosphate group and the sugar of adjecent molecules.

• The DNA molecules consist of 2 polynucleotide chain which are antiparallel, joined by pairs of bases to form a double helix.
• The pairings are always C and G, A and T . 3 hydrogen bonds formed between C and G. 2 hydrogen bonds between A and T.
• One strand run from 5 prime end to 3 prime end and the other strand run from 3 prime end to 5 prime end.

6) The 4 nitrogenous base found in RNA are U, A, C and G. U will pairs with A while C pairs with G.

7) There are 3 types of RNA : nRNA, tRNA, rRNA.

8) mRNa synthesized in nucleus from one part of DNA and associates with ribosomes and acts as template for protein synthesis.

9) Codon is a series of 3 adjacent bases in one polynucleotise chain which codes for a specific amino acid.

10) tRNA attach amino acid to its head according to the codon that is complementary to its anticodon.

11) Anticodon is a sequence of 3 adjacent nucleotides in tRNA that binds to a corresponding codon in nRNA during protein synthesis.

12) rRNA contains 3 bingding sites for protein synthesis ( P site, A site and E site).

13) A site hold the tRNA that carrying the next amino acid to be added to the polypeptide chain, P site hold the tRNA that carrying the growing polypeptide chain, E site discharged tRNa to leave the ribosome.

14) Short overview of DNA replication:

The two stands of DNA will separated and the free nucleotides attached to their complementary bases. DNA polymerase will fit the nucleotide to the single polynucleotide chain according to their complementary bases. The free DNA nucleosides add in in the 5 prime ro 3 prime direction.The new polycucleotide strand that formed continuously towards the replication fork is leading strand. The new polynucleotide chain that formed away from the replication fork is lagging strand. Okazaki fragments formed along the lagging strand. The okazaki fragments are then joined by the DNA ligase. When replication is completed, the 2 double-stranded daugther DNA molecules are formed.

15) DNA replication was accepted as semiconservative model because the replicated DNA will contain a parental strand and new strand.

16) The characteristics of genetic code:

• The code for almost all organisms is the same
• The code is degenerate.
• The code is non-overlapping.

17) Short overview of DNA transcription:

The DNA double strands unwind and RNa polymerase attaches to the transcribing DNA strand at the promoter site. As the RNA polymerase move along to the 3 prime end of DNA, complimentary nucleotides are added to it.When the enzyme move to another region of transcribing DNA strand, the double helix of DNA reforms behind it. Once reaching terminator, the enzyme deattached and the nRNA molecules moves away from DNA.

18) Translation is the process by which information encoded within mRNA is used to make specific polypeptide chain.

19) Start codon is the first codon in mRNA that translated by ribosome. The common start codon is AUG.

20) Stop codon is the codon in mRNA that signals the termination of translation. The common stop codon is UAA, UGA and UAG.

21) Wobble hypothesis states that the bases in first position of anticodon on tRNa is usually an abnormal base, like inosine. These abnormal bases able to pair with more than one type of nitrogenous base in the third position of the codon on mRNA. For example, inosine can pair with A, C and U. That's means only 32 tRNA are needed.

Activities: No other activities carried out except for teaching...^^

My own explorace:

1) Why pyrimidine must match with purines?

It is to ensure the center of DNA always contain 3 rings, ( Pyrimidine has one ring and purine has two rings)

2) Why introns need to remove?

It is because introns didn't carry any information for amino acid. If introns are not remove, wrong proteins will be translate or made.

3) The degenerate characteristics of genetic code means that some of the amino acids are coded for more than one codon.

4) James Watson and Francis Crick are the scientists that identified and discovered the double helix structure of DNA. 

Reflection:

Prof Khatijah was a cute and friendly lecturer. She kept told us about her story and experience because she doesn't want us to feel boring in her lecture. This lecture makes me recall back the genetics that I have learnt in from 6. Genetics is an interesting topic and I like this topic very much. 

12th Lecture : 7/11/14

Topic : Eukaryotic microorganisms

Notes:
1) Eukaryotic cell envelope

• consists of plasma membrane ( lipid bilayer )
• unlike peptidoglycan in bacteria and archaea
• cellulose, pectin and silica in photosynthetic algae
• cellulose, chitin and glucan in fungi
• Protozoa has pellicle, instead of cell wall
• Animals have glycocalyx surrounding the cell membrane

2) Structure of Eukaryotic cells

• Flagella ( long whip-like projection ) and cilia ( short whip-like projection )

- to move substances along cell surface

- 9+2 arrangement ( 9 pairs of microtubules in the ring and 2 single of microtubules at the center of the ring)

• Cell membrane

- have different membrane protein with the prokaryotic membrane

- have carbohydrates which important in cell-cell recognition

- contain sterols which increase resistance to osmotic lysis

- endocytosis ( encircles particles outside of cell) and exocytosis ( cells release secretions)

• Cytoplasm

- contain cytoskeleton which support, shape and movement

- cytoskeleton are made up of microfilament, microtubules and intermediate filament

- Microfilament consists of actin subunits, is the the smallest fibers

- Intermediate filament consists of fibrous subunits and anchor organelles in place, is the medium-sized fibres

- Microtubules consists of tubulin subunits, works in cell division and is the largest fibres

• Ribosomes

- the site of protein synthesis

- made up of proteins and rRNA

- found free in cytoplasm or associated to rough endoplasmic reticulum

- Eukaryotic ribosomes (80S) ( 60S large subunits, 40S small subunits )

• Organelles

a) Nucleus

- nuclear envelope ( double nuclear membrane)

- nuclear pores

- nucleoli ( dense region where ribosomes are made)

- DNA combined with histones can exist in two form : chromosomes and chromatin

- protect DNA

- ribosomes synthesis

b) Rough Endoplasmic Reticulum

- flat, interconnected, membrane sacs
- outer walls covered with ribosomes
- Synthesis and modification of protein
- Synthesis of cell and organells membrane

c) Smooth Endoplasmic Reticulum
- no ribosomes
- lipid synthesis
- breakdown of toxic compounds
- regulates sugar release from the liver into the blood
- calcium storage for cell and muscle contraction

d) Golgi Complex
- stacks of flattened membrane sacs
- work closely with ER to secrete proteins
- receive proteins in transport protein in ER
- modifies proteins
- packages and sends proteins to cell membrane
- packages digestive enzymes in lysosomes

e) Lysosomes
- released from golgi and optimum pH is about 5
- digest bacteria that can enter the cell
- self-destruction of cell
- contain enzymes to break various materials
- digestion of food particles
- destruction of foreign materials
- molecular garbage dump

f) Vacuole
- central vacuole, contractile vacuole, food or digestion vacuole
- central vacuole stores water, pigments, poisons, and starch
- contractile vacuole regulate water balance
- digestion vacuole fuses with lysosome to digest food particles

g) Chloroplast
- dics shape, with three membrane system
- site for photosynthesis
- carbon dioxide + water + sunlight = sugar + oxygen
-70S ribosome

h) Mitochondria
- rod shape organelle
- central role in ATP production through the degradation of organic compound
- contain their own DNA, 70S ribosome
- Sugar + Oxygen = Carbon dioxide + ATP + Water
- form inner and outer membrane, between the two membrane is inter membrane space, cristae is the inner membran extension, matrix is the inner liquid.

i) Peroxisomes
- oxidation of organic substances
- decompose hydrogen peroxide
- oxidize toxic substances

j) Centrosome
- pericentriolar and centrioles

3) Mitosis
- produces 2 daughter cells that are identical to the parent cell
Phases in mitosis:
a) interphase - chromosome are not visible
b) prophase - chromosome coil, nuclear membrane distingrate, spindle fibres form
c) metaphase - chromosome become aligned
d) anaphase - chromatids separate; the number of chromosome doubled
e) telophase - cells divide into two, chromosome uncoil, nuclear reform, spindle fibres diassembles.
f) G1 interphase - the chromosome has one chromatid
g) G2 interphase - the chromosome has two chromatid

4) Meiosis
- produce daughter cells that have half the number of chromosomes as the parent cell
- involve meiosis 1 and meiosis 2
- meiosis 1 - (the number of cells is doubled but the number of chromosome is not)
- meiosis 2 - (the number of chromosomes does not get reduced, this division is like mitosis)

Activities: Each group choose an organelle topic and conduct class activities based on the topic

My own explorace :
1) Amoeboid motion is a common mode of locomotion in Eukaryotic cells. It is like crawling-like movement involved the formation of pseudopodia. The cytoplasm slides and forms a pseudopodium in front to move the cell forward.
2) Why mitochondria need DNA and have the similar ribosomes to prokaryotic ribosomes?
Scientists believe that eukaryotes somehow being parasited by prokaryote and when this happened the prokaryotes somehow evaded being eaten by eukaryote and escaped from being killed by the eukaryotes' immune system. In fact, these prokaryotes actually provided such a large benefit to the new host eukaryote, then they were slowly incorporated into neccessary metabolism of the host cell. Therefore, the idea of a mitochondria being the descendants of prokaryotes is well-accepted.

Reflection:
We are familiar with these structures of eukaryotic cell and this lecture reminded me again about the structure of eukaryotic cell that I learnt in my Form 5 and Form 6. The activities conducted by each group in the class were interesting and meaningful. These activities made the lessons not to be so boring and easier for me to memorise and understand the structures.

11th Lecture: 31/10/14

Topic: Algae and Fungi

Notes:
1) Fungi are spore-bearing organisms which exist as a single kingdom.
2) Most Fungi are multicellular except for yeast which are unicellular.
3) Cell wall of fungi is made up of chitin and they store glycogen. They can reproduce sexually and asexually.
4) Fungi can found in primary terrestial and aquatic environment.
5) The body structure of a fungus is called thallus. Thallus consists of long,branched hyphae filaments, tangled into a mycelium mass.
6) The feeding forms of fungi : Mutualistic, Parasitic, saprobic.
7) Telomorphic Fungi produce sexual and asexual spores only. Anamorphic spores procude asexual spores only.
8) Fungus can undergo mitosis to produce a daughter cell through asexual reproduction (budding).
9) Sexual reproduction of fungus involved gametes and spores. Homothallic :Sexually-compatible gametes are formed on the same mycelium. Heterothallic : require outcrossing between different,yet compatible mycelia.
10) Sexual spores types: Zygospores ( spores enclosed in a thick wall), Ascospores ( spores prodeced by ascus) and Basidiospores (formed externally at a base of basidium).
11) Summary of the life cycle of fungi:
Asexual reproduction: Mycelium undergo mitosis to produce haploid spore-producing structure. This structure later on produce haploid spores to germinate.
Sexual reproduction: Mycelium first undergoes plasmogamy (cytoplasmic fusion) then karyogamy ( nuclear fusion). Between plasmogamy and karyogamy is dikaryotic stage (n+n). After karyogamy, diploid zygote undergo meiosisto produce haploid spore-producing structure. This structure will produce haploid spores to germinate later.
12) Fungi consist of 5 phyla:

• Chytridiomycota ( cannot see with naked eye)
• Zygomycota ( mostly mycorrhizae)
• Ascomycota
• Basidiomycota ( mostly mycorrhizae)
• Microsporidia

13) The example of chytridiomycetes is anaerobic rumen fungi. They are neocallimastigales, obligate anaerobes. They can decompose cellulose, break sown lignin deposits into smaller pieces and produce zoospores.
14) In Zygomycota, most of the Fungi are decomposers and mutualists (mycorrhizae). They form coenocytic hyphae, zygosporangia. The example of zygomycota is Rhizopus stolonifer, the bread mold which under genus Rhizopus.
15) Glomeromycota comsidered zygomycetes by some . They form intracellular associations within roots for almost all herbaceous plant and tropical plants.
16) Zygomycota and chytridiomycota are paraphyletic.
17) Ascomycetes are sac fungi, human and and plant pathogens. They produce conidia in asexual reproduction and form ascus with ascospores in sexual reproduction.
18) Genus aspergillus is one of the genus of ascomycetes. They are ubiquitous and they can cause aspergillosis.
19) The another example of ascomycete is Claviceps purpura. C.purpura is parasite on higher plants and they can cause ergotism. Ergotism is the effect of long term ergo-poisoning due to the ingestion of alkaloids that produce by C.purpura that infects rye and other cereals.
20) In Basidiomycota, basidiomycetes are club fungi and they produce basidiospores. They are decomposers and some of the mushrooms are edible.
21) Urediniomycetes and Ustilaginomycetes are the classes under Basidiomycota and they are dimorphic and some of them are human pathogens.
22) Microsporidia are obligate intracellular fungi parasites that infect insects, fish and humans. They contain chitin, trehalose, mitosomes but lack mitochondria, peroxisomes and centrioles.
23) Mycorrhizae is the mutualistic association between plant root and fungi. This association can increase the surface area and growth potential for plant while fungi can feed from tissues of the plant.
24) Lichens are mutualistic relationship between algae and fungi. The algae produce food and the fungus provides protection, water and minerals.
25) There a 3 types of lichens:

• Foliose lichens: leaf-like
• Fruticose lichens: hair-like
• Crustose lichens: grow flat to the surface

26) The fungus in lichens is called mycobiont and the photosynthesizing organism is called a photobiont. Most of the photobiont are algae. Mycobiont adsorb nutrients and photobiont synthesize organic nutrient from carbon dioxide.
27) Yeast under Ascomycota and Basidiomycota. Yeast reproduce asexually by budding, and few by binarry fission. The famous yeast to make bread is Saccharomyces cerevisiae.
28) Dimorphic Fungi undergo dimorphism which is the two form of growth either as mold or yeast.

Activities: Algae and Fungi Crossword.

My Own Explorace:
1) Eumycota means true fungi. It is to differentiate from myxomycota (fungus like slime mold) .
2) Is any fungus exist in the desert? Yes, it is. Desert fungi create symbionts with other host to ensure survival. They resistant to high temperature, dryness and low nutrition. The genus Coccidioides is a soil fungus that live in desert. Each species create hyphae and spore in the soil. After the spores being disturbed by dust storm, the spores are air-borne. People that inhale the spores may causes Coccidiodomycosis (valley fever).body. Cutaneous mycoses: These diiseases extend deep into the epidermis such as hair and nails.
3) Mycosis are diseases that causes by fungus. Subcutaneous mycoses: These kind of diseases may infect dermis, muscle and fascia. Systemic mycoses: These kind of diseases can affect all over the Superficial mycoses: These disease affect the skin of young people.
4) Aerial mycelium : The portion of mycelium that grows upward or outward from the surface of the subtrate.
5) Coenocytic means multinucleated.
6) Dikarya is the subkingdom of Fungi that includes the phyla Ascomycota and Basidiomycota, both which in general produce dikaryons.
7) Paraphyletic means having the same ancestor.
8) These are the truffles.

9) Conidia are asexual spores that usually form at tip or side of hyphae.
10) Obligate refers to parasites that cannot complete its life cycle without exploiting a suitable host.
11) Cryptococcosis is the most common fungal disease in HIV-infected person and it is the AID-defining illness for 60%-70% of HIV-infected patients.
12) Vampyrellids (vampire amoeba) are predators of fungi because it can detroy the fungi by making holes on Fungi.

Reflection:
I learned a lot from the preparation until the exhibition day of Thank A Microbe. First, I learned how to design poster using power point in A1 size and how to create video by adding background description. I felt lazy to go Bukit Expo because Bukit Expo is far away from my kolej. Due to this project, I have a chance to re-visit Bukit Expo to capture our video. My members and I were having a lot of fun there. Besides that, my group members and I worked together so well. Due to this project, we knew about each other more well and I really appreciate the efforts they did to make this exhibition success. Finally, I learned that preparation is important. I thought I had done enough research and preparation for the presentation. Unfortunately, we can't answer the questions from the judges. I felt not satisfied about this. I think we can do better when facing the questions from the judges. Last, I would like to thanks Dr.Wan for guiding us along the preparation until the exhibition day. Thanks for giving a chance to do this challenge and we did it ! For the fungi lecture, there are a lot of terms that I really not familiar with. I will try my best to understand the terms and memorise the terms.