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.

10th Lecture : 14/10/14

Topic: Algae

1) Algae under kingdom protists because they are hard to define.

2) Algae different from plant because they don’t have vascular system.

3) Algae different from animal because they are autotrophs.

4) Algae can be unicellular or multicellular.

5) Algae contain chlorophyll which make them able to make food.

6) Algae live in aquatic or terrestial.

• Planktonic - suspended in aqueous environment
• Benthic - attached and living on the bottom of water
• Neutonic - at water-atmosphere interface

7) Most of the algae have cell wall composed of cellulose,  except for diatom which are made of silica. Sometime chitin or no cell wall.
8) Euglena have single flagella, chlorophyta have two or four polar flagella. For dinoflagellates, they have two flagella of different length and point of insertion.
9) All algae carry out asexual reproduction (fragmentation, spores, binary fission) but not all algae able to carry out sexual reproduction ( oogonia fuse with antheridia to form zygote).

10) Algae can divided into 5 phyla:

• Chrysophyta - diatoms
• Euglenophyta
• Pyrrhophyta - dinoflagellates
• Charophyta 
• Chlorophyta - Green

11) Chlorophyta

• green
• cellulose cell wall
• unicellular or multicellular
• chloropyll a or b
• store glucose polymer
• gave rise to terrestial plants

12) Rhodophyta ( changed to kingdom plantae ) 

• red
• mostly cellular
• cellulose/agar cell wall
• sexual reproduction'
• sstore glucose polymer
• chlorophyll a and d, phycocyaninm phycoerythrin
• red pigment absorb blue light

13) Phaeophyta ( changed to kingdom plantae )

• brown
• macroscopic
• chlorophyll a and c, xanthophylls
• multicellular
• cellulose or algin cell wall
• sexual reproduction
• store carbohydrate

14) Chrysophyta

• golden-brown algae
• produce domic acid
• chlorophyll a and c
• unicellular
• peptin and silica cell wall
• sexual reprodution
• store oil

15) Pyrrophyta

• unicellular plankton
• brown
• 2 flagella in perpendicular opposite grooves
• some produce neurotoxins
• can cause red tides
• chlorophyll a and c
• cellulose cell wall
• store starch

16) Euglenophyta

• green
• unicellular flagellated
• chlorophyll a and b, carotene
• can spontaneous lost chlorophyll in dark - heterotrophic organisms
• no cell wall
• rigid plasma membrane - pellicle
• no sexual reproduction
• store glucose polymer

17) Seaweed are marine benthic algae that can provide habitat for marine communities, and human food to make various products.

18) Phytoplankton are primary producers of the ocean because phytoplankton converts carbon dioxide into protoplasm to consumed by zooplankton.

19) Algal bloom will disrupt higher links of local food web and cause the production of neurotoxin.

Activitiy : Exchange our own notes with group members.

My own explorace:
1) Photoautotrophs are the orgainsms use the energy from light to carry out various cellular metabolic processes.
2) Endosymbionts are any organisms that lived within the body or cell or other organisms. Corals and dinoflagellates establish an symbiotic relationship where the dinoflagellates provide fixed carbon to corals while algae receive various nutrients from corals.
3) Members of Rhodophyta have a characteristic clear red or purplish color are due to the pigments called  phycoerythrin, which is well suited to absorb the blue light that penetrates deeper into water than the other colors of light.
4) Red tide is a phenomenon known as algal bloom when it is caused by dinoflagellates and the bloom takes on a red or brown colour. Some red tides are harmful because it associated with the production of neurotoxins. It kills many manatees every year.

Manatee

Reflection on this topic:

The mood in the class was quite down. The reasons may due to the Kenegaraan test but I think most of us were already in holiday mood, not study mood, hahaha..I think people shouldn't look down on these small tiny algae. An algae looked like nothing but a large number of algae can make things worse. Red tides which caused by large number of dinoflagellates can killed a lot of marine organisms, even the cute manatee. T.T 

9th Lecture: 10/10/2014

Topic: Test 1 and Protozoa

Notes:
1) Protozoa are eukaryotes, no chlorophyll, unicellular and lack of fruiting body.
2) Protozoa can be parasitic, pathogenic and predatory.
3) Protozoa can be aerobic, anaerobic and chemoheterotrophic
4) Protozoa are colourless and motile, but apicomplexa are not motile in mature form.
5) Protozoa can reproduce sexually and asexually by fission, budding and schizogony.
5) The microscopic of protozoa is 10 to 200 micrometer.
6) Protozoa occur singly or in colonies.
7) Protozoa can pigmented or not pigmented.
8) Protozoa may swim freely or in contact with a substratum. Some of the protozoa are capable of encystment.
9) Phylum:
      Saya-Sarcomastigophora
      Lupa- Labyrinthomorpha
      Akan- Apicomplexa
      Makan- Microspora
      Ayam- Ascetospora
      Mymy- Myxozoa
      Cili- Ciliophora
10) Dinoflagellates and Euglenoids are capable of photosythesis.
11) Protozoa obtain fruits through phagocytosis, pinocytosis, ingestion and absorption.
12) There are four major groups in protozoa: Archaezoa, Rhizopoda, Ciliophora, Apicomplexa.
13) Archaezoa are flagellated, parasitic and live in fresh water.
14) Rhizopoda are move by pseudopods, undergo phagocytosis and live in freshwater. Example:Amoeba
15) Ciliophora possess cilia, live in freshwater and marine, contain macronuclei( production of mRNA)and micronuclei (sexual reproduction) , having the presence of gullet ( ingest particulate materials), Example: Paramecium
16) Apicomplexa are primarily animal parasites, food absorbed through the outer wall and having complex life cycle. Example: Plasmodium

Activities: Test 1 and presentation about the best way to study protozoa.

My own explorace:
1) Substratum is a surface which cell attaches to, especially when the cells is growing or moving.
2) Chemotrophs are organisms that obtain energy by the oxidation of electron donors in their environment. They can be autotrophic or heterotrophic.
3) Encystment is the process of being enclosed by a cyst. Cyst is a resting or dormant stage of microorganisms. Cyst helps microorgsnisms to survive in unfavourable environmental condition in which the cell activities will be slowing down. Encystment also help the microbes to disperse easily from one host to another.
4) Pseudopods are temporary projections of eukaryotic cell membranes or unicellular protists.
5) Schizogony is the asexual reproduction of sporozoan by multiple fission of nucleus of the parasite followed by segmentation of the cytoplasm.
6) Most of the dinoflagellate are marine plankton but they are common found in freshwater as well. Most of them are photosynthetic.

Reflection on this topic:

After the test, I checked my notes and I found that I got some objectives wrong. I was getting mad because I did read and memorised the notes and I still got these wrong. Dr,Wan was right. We need to really understand everything well but not just memorised. I like the study method of Choy's group but I need him to record that song so that we able to sing it again and again. I also like the study method of our group: Fill in the blanks !! It is really work by fill in the blanks after we have studied the notes.

8th lecture: 7/10/14

Topic: Inclusions

Notes:
1) The main purpose of inclusions are to reserve deposits when it's plentyful and use it when it's deficient.
2) Metachromatic granules also known as volutin and used in the synthesis of ATP.
3) Metachromatic granules stain red with certain blue dyes.
4) Polysaccharide granules consist of glycogen and starch. Glycogen and starch can be differentiated by iodine. Glycogen granules will indicate reddish brown colour while starch will indicate blue colour.
5) Lipid inclusions act as storage material and can be revealed by Sudan dyes.
6) Sulfur granules derive energy by oxidising sulfur and sulfur-containing compounds.
7) Carboxysomes used for carbon dioxide fixation during photosynthesis.
8) Magnetosomes contain iron oxide that act like magnet. It is to protect the cell against hydrogen peroxide accumulation and to look for oxygen concentrated area.
9) Gas vesicles also known as gas vacuole. We called it gas vesicles when it is found in prokaryotes while in eukaryotes we called it gas vacuole. It is to provide buoyancy for aquatic prokaryotes and mostly found in photosynthetis group of prokaryotes.
10) Endospores are formed during harsh condition by some bacteria and it will germinate during suitable condition.
11) Endospores cannot be destroyed easily. They resist to chemicals, radiation, heat and acids.
12) Endospores contain substances that are absent from vegetative cells especially dipicolinic acid. This substance give all the resistance to endospores.
13) Although spores are resistant to dye, they still can be stained with malachite green.

Activities: Short Quiz and decide the adapoted microbes.

My own explorace:
1) Corynebacterium diphtheriae is the pathogenic bacterium that causes diphtheriae. Corynebacterium diphtheriae is a gram positive bacteria. Diphtheria is an upper respiratory illness. Diphtheria toxin is produced by Corynebacterium diphtheriae only when infected with a bacteriophage that integrates the toxin-encoding genetic elements into the bacteria.
2) Fungus uses energy to produce nutrients and spores.
3) Carbon dioxide fixation also called Calvin cycle and it is light-independent reaction. The key enzyme of this cycle is called RuBisCo.
4) Microbial nutrition are substances that microbes used to survive. If the source of carbon come from carbon dioxide and the source of energy come from sunlight, this organisms are called phototrophs.
5) Hydrogen peroxide is toxic and it is found in hair dyes. Human and aerobic microbes have the enzyme to neutralise hydrogen peroxide. The enzyme is celled peroxidase. But, peroxidase are not found in anaerobic microbes. Therefore, magnetosomes are found in anaerobic microbes to protect them against hydrogen peroxide accumulation.
6) Microaerophile is microorganism that requires oxygen to survive, but at a lower concentration than that contained in the atmosphere. A faculatative anaerobes is an organisms that makes ATP by aerobic respiration if oxygen is present, but is capable switch to anaerobic respiration if oxygen is absent. Too much oxygen is not toxic for faculatative anaerobes but too much oxygen is toxic for microaerophile.
7) Clostridium tetani is anaerobis, gram positive bacterium that causes tetanus.
8) Desiccation is the state of extreme dryness, or the process of extreme drying. Microbes that able to survive in desiccation are called xerophilic microbes. Xerophilic microbes are mostly archaea.
9) Clostridium perfringens cause gas gangrene which is a bacterial infection that produces gas in tissue in gangrene. Gas gangrene can caused myonecrosis ( muscle tissue death). The only treatment is through amputation of damaged arm or leg to control the spread of infection.
10) This is the video about the formation of endospores:
http://www.youtube.com/watch?v=7zCQLITFEb0

Reflection on this topic:
I have learnt how strong is the endospore. I understand why clostridium botulinum have the potential to act as biological weapons. Endospores can be anywhere and everywhere.