normal_post - Online Lessons: Molecular Biology - Science and Research Author Topic: Online Lessons: Molecular Biology  (Read 2341 times)

Lorenzo

  • SUPREME COURT
  • THE LEGEND
  • *****
  • avatar_240_1418794287 - Online Lessons: Molecular Biology - Science and Research
  • Posts: 54226
  • medal1 - Online Lessons: Molecular Biology - Science and Research medal2 - Online Lessons: Molecular Biology - Science and Research medal3 - Online Lessons: Molecular Biology - Science and Research medal4 - Online Lessons: Molecular Biology - Science and Research medal5 - Online Lessons: Molecular Biology - Science and Research medal6 - Online Lessons: Molecular Biology - Science and Research
  • Be the change you want to see in the world...
    • Share Post
xx - Online Lessons: Molecular Biology - Science and Research
Online Lessons: Molecular Biology
« on: January 23, 2008, 09:32:36 AM »
This will be an online review of Molecular Biology for this Spring Semester. The data included in this thread will follow the time chronology of lessons learned and taught in Molecular Biology 305. If interested, follow through, if you have further questions about the basis of the periodic lessons, feel free to ask it here or PM me; either way it is up to you.

I'm starting this lesson thread for practical purposes, to keep the information flowing--


That said, lets begin!

Linkback: https://tubagbohol.mikeligalig.com/index.php?topic=8818.0

Lorenzo

  • SUPREME COURT
  • THE LEGEND
  • *****
  • avatar_240_1418794287 - Online Lessons: Molecular Biology - Science and Research
  • Posts: 54226
  • medal1 - Online Lessons: Molecular Biology - Science and Research medal2 - Online Lessons: Molecular Biology - Science and Research medal3 - Online Lessons: Molecular Biology - Science and Research medal4 - Online Lessons: Molecular Biology - Science and Research medal5 - Online Lessons: Molecular Biology - Science and Research medal6 - Online Lessons: Molecular Biology - Science and Research
  • Be the change you want to see in the world...
    • Share Post
xx - Online Lessons: Molecular Biology - Science and Research
Reply: Online Lessons: Molecular Biology
« Reply #1 on: January 29, 2008, 06:19:09 AM »
In order to have a firm grip in the concepts within the broad field of Molecular biology, one has to understand that this study encompasses the attention on those aspects of genetic material and how it is perpetuated and expressed in the forms of RNA and protein. The general topics that will be covered, therefore, are replication, transcription, and RNA processing.

The solid foundation of molecular biology lies in the simple yet complex nature of the DNA structure, which are composed of multiple functional groups and properties, namely:
1) Methyl
2) Hydroxyl
3) Carbonyl
4) Amines
5) Amides
6) Phosphates

Methyls are rather simplistic, its non-polar and it is hydrophobic, it likes water because H20 itself is a polar molecule; and the hydrophobicity of H20 allows the synthesis of hydrogen bonding: so long as there are instances of
a) electronegative atom
b) hydrogen covalently bonded to an electron atom.

Carbonyl's are necessary due to their Carbon to Oxygen double bond, it is polar non-charged but whole group is polar-charged; ionic and Hydrogen bonding interactions are delineated within.

For amines, just know that there are conjugated bases, as well as conjugated acid forms or as what I tell my students (generally known as basic groups).
Amines on the other hand is rather interesting because it is seen in almost every protein structure, both oxygens and nitrogens within in are electronegative, there is a big electron cloud around the whole molecule (or other wise known in biochemical and thermodynamics as "partial" double bound character). Due to the Carbon-Nitrogen partial bond, there is no rotation around this structure, and proteins within our bodies are able to develop a structure due to the C-N bond in the amides.

Phosphates are another key structural component of DNA; it is what makes DNA acidic, it is always attached to a nucleotide, and most phosphates are usually attached to things. One thing that I love to reiterate is the 'Divinity' of phosphates, from it comes all forms of energy: Phosphates are groups where bonding between the phosphate are easily broken AND it is the breaking of these phosphate-phosphate bonds that releases energy -> which in turn allows the making of reactions.
ATP (adenosine triphosphate) are sources of energy that is necessary for every biotic movement is actually a source of energy that is created by phosphates. Without phosphates, proteins will never bond to a DNA sequence of structures, there will be no ribosome organelle that produces the proteins to allow the induction of RNA primers to allow the translation and transcription of the helical bend. That is why we refer to the term "Divinity" of phosphate. Without it, everything in the said organism would be in stasis. Death as a biological and absolute law would manifest in the said organism, species, population, etc.

The Building Blocks: Nucleotides

There are two different types of nitrogenous bases that composes and make up the nucleotides, namely purines and pyrimidine. There are basic structural conformity that differentiates the two, purines are larger 2 ring structures, whereas pyrimidines are a singular aromatic ring.

The 3 major pyrimidines: Cytosine, Thymine => DNA
                                  Cytosine, Uracil => RNA

The 2 major purines: Adenine, Guanine

There are also sugar groups that differs from one another; namely in their grouping
DNA -> Deoxyribose (sugar type)
RNA -> Ribose (sugar type)

Also it is necessary to understand that nucleotides are nucleosides + a phosphates (phosphate + sugar + base)
What is a nucleoside? It is a nucleotide that is missing a phosphate group
The bond between the nitrogenous base and water is called: N-glycosidic bond

When referring to nucleotide know that sugars are labeled in 5' (five prime) to 3' (three prime)

What determines directionality of these compounds?
5'-> 3', it is the sugars
Sugars are joined to each other via a phosphodiester bond, and thus DNA has regions composed of the major grooves and minor grooves. The major grooves are larger spaces observed in the anti-parallel double helix with no sugar or phosphate backbone face it; minor grooves have sugars attached to it.


The following are uploaded images from the text book to better illustrate the said concepts


Picture1 - Online Lessons: Molecular Biology - Science and Research
The helical anti-parallel structure of DNA, you can notice the large spaces are the major grooves, the smaller spaces are the minor grooves (which has sugars attached to it)

Picture2 - Online Lessons: Molecular Biology - Science and Research
Proliferation of genetic sequence from a phage parasite onto a host cell; replication explained in here.

Picture3 - Online Lessons: Molecular Biology - Science and Research
The major nucleotidic structures. The top structures, as you can see are 2 aromatic rings, which are part of the purine groups, the lower structures are singular aromatic rings, part of the pyrimidine group. These base groups are what composes the complex sequential nature of our genetic codets. "The fingerprints of GOD," as what I like to say. :)

Picture4 - Online Lessons: Molecular Biology - Science and Research
Two sugars. One is the Deoxyribose, the sugar found within eukaryotic species (higher leveled organisms in the echelon of the continuum of life; ex animals, tertiary botanic species)
The other sugar is Ribose, the sugar found within most prokaryotes or 'lesser' organisms, bacteria, virus, fungi etc

Picture6 - Online Lessons: Molecular Biology - Science and Research
The phosphodiester bonds, the phosphitic bonds within nucleosides. These provide the basis for DNA structure, or energy sequestration, the breakage of these Phosphate bonds literally gives off 'ATP energy' that is essential for life itself. As i said earlier, 'divinity of phosphates'

Picture7 - Online Lessons: Molecular Biology - Science and Research
A clearer picture of the phosphodiester bonds

Picture8 - Online Lessons: Molecular Biology - Science and Research

Picture9 - Online Lessons: Molecular Biology - Science and Research
Broader picture, you can actually see in the upper left hand image of the sugars, the phosphates, the nucleotides in full combination, all are complementary. The lower image shows the 'minor' groove, and the 'major' groove. Note that the minor groove has sugars attached to its side, while none are found in the major groove.



Next lesson will be on Protein Structure

Lorenzo

  • SUPREME COURT
  • THE LEGEND
  • *****
  • avatar_240_1418794287 - Online Lessons: Molecular Biology - Science and Research
  • Posts: 54226
  • medal1 - Online Lessons: Molecular Biology - Science and Research medal2 - Online Lessons: Molecular Biology - Science and Research medal3 - Online Lessons: Molecular Biology - Science and Research medal4 - Online Lessons: Molecular Biology - Science and Research medal5 - Online Lessons: Molecular Biology - Science and Research medal6 - Online Lessons: Molecular Biology - Science and Research
  • Be the change you want to see in the world...
    • Share Post
xx - Online Lessons: Molecular Biology - Science and Research
Re: Online Lessons: Molecular Biology
« Reply #2 on: February 07, 2009, 08:41:00 PM »
Protein structures:

Primary
Secondary
Tertiary
Quaternary


Manong JOSE

  • STUDENT
  • *
  • avatar_781 - Online Lessons: Molecular Biology - Science and Research
  • Posts: 259
  • Pakighiusa, Pakigdait ug Pakiglambigit
    • Share Post
xx - Online Lessons: Molecular Biology - Science and Research
Re: Online Lessons: Molecular Biology
« Reply #3 on: February 07, 2009, 09:30:11 PM »
Sir Lorenzo, I like this thread for I am interested to learn more about Molecular Biology. However, I could not relate to other concepts you have mentioned because, I guess, there are previous concepts that I have to learn first before this one. I can recall only a little about my Chemistry class before.

As David Ausubel proposed, "Learners will learn more if they could find connection between existing knowledge and the lesson to be learned." For learning to be remarkable, it has to be meaningful and meaningfulness can only be provided through connection.

I am not wondering why, of all the sciences, Physics is the one that I like the most. It's because learning Physics is just like learning mathematics. Acceleration and velocity can be calculated through differentiation (differential calculus) and the change of the temperature of a certain body can be computed through differential equations. Newton likes Physics and Mathematics. He has great contribution in the field of Physics and Calculus.

Nevertheless, BRING IT ON Sir! I will follow this thread and will ask you if I have any confusion. For now, I have to read the entire lesson again. :D :D :D

Lorenzo

  • SUPREME COURT
  • THE LEGEND
  • *****
  • avatar_240_1418794287 - Online Lessons: Molecular Biology - Science and Research
  • Posts: 54226
  • medal1 - Online Lessons: Molecular Biology - Science and Research medal2 - Online Lessons: Molecular Biology - Science and Research medal3 - Online Lessons: Molecular Biology - Science and Research medal4 - Online Lessons: Molecular Biology - Science and Research medal5 - Online Lessons: Molecular Biology - Science and Research medal6 - Online Lessons: Molecular Biology - Science and Research
  • Be the change you want to see in the world...
    • Share Post
xx - Online Lessons: Molecular Biology - Science and Research
Re: Online Lessons: Molecular Biology
« Reply #4 on: February 07, 2009, 09:45:55 PM »
Jose,

The structures that were mentioned above just talks about the nucleotides; and the sugar bases that composes the DNA helix.

Know that in a given DNA we have 4 possible bases:
1) Adenine
2)Guanine
3) Thymine
4) Cytosine

Now these bases are subcatechorized according to their conformation (which is due to electrospecificity) as well as to their aromatic structure (meaning, a single or double rigned form).

There are 2 forms:
1) Purines
2) Pyrmidines

The purines are composed of the Guanine and Adenine
The pyrmidines are composed of Cytosine and Thymine

a good way to remember the difference is "CING TUT MADE PYRAMIDS"
this way we remember that C (cytosine) and T (thymine) are of the pyramidal group

When these sugar bases are paired, they have specific conformation with one another.

Meaning that A goes with T
And G goes with C
These unions are facilitated via a Hydrogen Bond.

The variants of ACGT formats is what makes and composes our DNA (coupled with a stable phosphodiester bond, which composes the backbone of the DNA structure).

I shall expound on this later.

Glad to discuss this with you, Jose.
Please, just call me Lorenzo.
Like you, I am nothing but just an ordinary student. :)



LET US LEARN TOGETHER!

Manong JOSE

  • STUDENT
  • *
  • avatar_781 - Online Lessons: Molecular Biology - Science and Research
  • Posts: 259
  • Pakighiusa, Pakigdait ug Pakiglambigit
    • Share Post
xx - Online Lessons: Molecular Biology - Science and Research
Re: Online Lessons: Molecular Biology
« Reply #5 on: February 07, 2009, 09:55:15 PM »
Can you give simple examples of those 4 possible bases of DNA? Like Sodium Chloride (salt) and Hydrochloride (acid), do they have common names?

I'm a noob and sorry for I have plenty of questions.

Lorenzo

  • SUPREME COURT
  • THE LEGEND
  • *****
  • avatar_240_1418794287 - Online Lessons: Molecular Biology - Science and Research
  • Posts: 54226
  • medal1 - Online Lessons: Molecular Biology - Science and Research medal2 - Online Lessons: Molecular Biology - Science and Research medal3 - Online Lessons: Molecular Biology - Science and Research medal4 - Online Lessons: Molecular Biology - Science and Research medal5 - Online Lessons: Molecular Biology - Science and Research medal6 - Online Lessons: Molecular Biology - Science and Research
  • Be the change you want to see in the world...
    • Share Post
xx - Online Lessons: Molecular Biology - Science and Research
Re: Online Lessons: Molecular Biology
« Reply #6 on: February 07, 2009, 10:05:14 PM »

These are good questions, every question is welcome.

We have to first understand that DNA (deoxyribonucleic acid: meaning that an O2 was cleaved from the 3' to 5'  position from the ribose acid). In DNA we can only have 4 bases.

The bases are: Adenine, Guanine, Cytosine, and Thymine.

However, in RNA (Ribonucleic acid) the bases are: Adenine, Guanine, Cytosine and Uracil. Uracil merely replaces Thymine in the RNA complex.

Know that RNA is produced and utilized during the transcription process where the DNA Helix is unwinded by the DNA Helicase, and the two regions are segregated as the template strand or the coding strand. In the coding strand, the RNA will bind with it to trascribe the protein.

Jose, remember the DOGMA of Genetics and Molecular Biology:
DNA--> RNA--> PROTEINS

But DNA can self replicate and RNA can go back into DNA vis-a-vis the help of the enzyme Reverse Transcripterase.


Lorenzo

  • SUPREME COURT
  • THE LEGEND
  • *****
  • avatar_240_1418794287 - Online Lessons: Molecular Biology - Science and Research
  • Posts: 54226
  • medal1 - Online Lessons: Molecular Biology - Science and Research medal2 - Online Lessons: Molecular Biology - Science and Research medal3 - Online Lessons: Molecular Biology - Science and Research medal4 - Online Lessons: Molecular Biology - Science and Research medal5 - Online Lessons: Molecular Biology - Science and Research medal6 - Online Lessons: Molecular Biology - Science and Research
  • Be the change you want to see in the world...
    • Share Post
xx - Online Lessons: Molecular Biology - Science and Research
Re: Online Lessons: Molecular Biology
« Reply #7 on: February 12, 2009, 03:37:49 PM »
Again, one thing that is rather interesting in Molecular Biology or genetics is the Recessivisity and dominance of our genes. Through the basis of meisos and mitosis, we have chromosomal cross-overs, which leads to genetic variance, which leads to, in the organismal form, degrees in levels of phenotypic peculiarities due to genotype.


Do you want to know more about what causes and inhibits recessivisity and dominance?


Lorenzo

  • SUPREME COURT
  • THE LEGEND
  • *****
  • avatar_240_1418794287 - Online Lessons: Molecular Biology - Science and Research
  • Posts: 54226
  • medal1 - Online Lessons: Molecular Biology - Science and Research medal2 - Online Lessons: Molecular Biology - Science and Research medal3 - Online Lessons: Molecular Biology - Science and Research medal4 - Online Lessons: Molecular Biology - Science and Research medal5 - Online Lessons: Molecular Biology - Science and Research medal6 - Online Lessons: Molecular Biology - Science and Research
  • Be the change you want to see in the world...
    • Share Post
xx - Online Lessons: Molecular Biology - Science and Research
Re: Online Lessons: Molecular Biology
« Reply #8 on: February 17, 2009, 11:29:28 PM »
Another topic worthy of discussion is the viral ability to 'decode' and 'take over' genetic transcription and translation of cells in an organism to benefit viral replication.

An direct and solid proof of evolutionary processes. Virus' have been a factor since the pre-primordial epoch. Even before the rise of sentient beings.


Lorenzo

  • SUPREME COURT
  • THE LEGEND
  • *****
  • avatar_240_1418794287 - Online Lessons: Molecular Biology - Science and Research
  • Posts: 54226
  • medal1 - Online Lessons: Molecular Biology - Science and Research medal2 - Online Lessons: Molecular Biology - Science and Research medal3 - Online Lessons: Molecular Biology - Science and Research medal4 - Online Lessons: Molecular Biology - Science and Research medal5 - Online Lessons: Molecular Biology - Science and Research medal6 - Online Lessons: Molecular Biology - Science and Research
  • Be the change you want to see in the world...
    • Share Post
xx - Online Lessons: Molecular Biology - Science and Research
Re: Online Lessons: Molecular Biology
« Reply #9 on: February 20, 2009, 04:50:11 PM »
One of the patients that we observed the other day was suffering from enterocyting bacterial infection. Result ni of gram-negative bacterial infection.

And in dealing with such bacteria, we will use antibiotics that are hostile to the membranes of the gram negative bacterium. As these organisms, over the onslought of the evolutionary proceses have developed defense mechanisms: per se production c-AMP-CAP complex repressors of the targeted antibiotic.

Literally meaning that within their genetic processes, they are able to turn 'off' the repressors that bind to the start site of transcription in the operator/promotor complex.

Pseudomonoas, e.coli, streptococus are but an example of such anti-repressive abilities.

It is an evolutionary trait.



Share via facebook Share via linkedin Share via pinterest Share via tumblr Share via twitter

xx
We share a molecular armor with coral reefs

Started by hubag bohol on Science and Research

2 Replies
463 Views
Last post April 27, 2016, 09:53:43 AM
by hubag bohol
 

SMF spam blocked by CleanTalk
Powered by SMFPacks SEO Pro Mod | Sitemap
Mobile View
SimplePortal 2.3.7 © 2008-2019, SimplePortal