• 3rd July
    2014
  • 03

Post-Transcriptional Processing

Only in the Nucleus for Eukaryotes
Primary transcript processed in 3 ways:
1. ADDition of nucleotides
2. DELETion of nucleotides
3. Modification of Nitrogenous Bases
5’ cap and 3’ Poly A tail
snRNP and the Spliceosome of Doom!
INtrons = IN nucleus
EXtrons = EXit the nucleus

DNA TECHNOLOGY

Clone Library = plasmid and replication

Polymerase chain reaction (PCR) : ‘fast’ cloning

Heat to denature
Mix with primers, let cool = primers hybridize
Add polymerase to amplify complementary strands

Southern Blot

1. Chop up DNA
2. Efield to spread out pieces by SIZE
3. Blot it!
4. Add Radioactive DNA or RNA Probe
5. Visualize on radiographic film 
GENETIC CODE
Degenerative – more than one series of nucleotides may code for ANY A.A.
Unambigous = one series of nucleotides = one A.A.
Universal code!
START! AUG
STOP! UAA, UAG, UGA
4^3 = 64 
Ex. protein of 100 A.A. = there are 20^100 possible amino acids sequences for the protein 
  • 7th May
    2014
  • 07
  • 4th May
    2014
  • 04
I am a high school junior and I am taking AP Biology. The test is coming up soon and there is so much information to study that I have no idea how to study for it. Do you know a studying technique that would be effective for large amounts of information?

Asked by: medically-brunette

Study the big overarching stuff from each topic. Make a study guide composed of every topic and break it down into what is important for every topic! Hope that helps!

  • 25th April
    2014
  • 25
Great Review of the Eukaryotic Cell! 
Nucleus

Defining characteristics (membrane bound nucleus, presence of organelles, mitotic division)


Defining characteristics = what sets eukaryotes apart from prokaryotes.




Eukaryotes have a true nucleus (membrane-bound), while prokaryotes don’t.




Eukaryotes have membrane-bound organelles (ER, Golgi, lysosomes, mitochondria), prokaryotes don’t.




Eukaryotes divide by mitosis (all them chromosomes line up and stuff), prokaryotes undergo binary fission (no chromosomes, just a circular ring of DNA, no need for complex mitosis)



Nucleus (compartmentalization, storage of genetic information)


compartmentalization: nuclear membrane / nuclear envelope surrounds the nucleus.




genetic information is stored inside the nucleus as DNA.



Nucleolus (location and function)


location is a region inside the nucleus.




function is to transcribe ribosomal RNA (rRNA).



Nuclear envelope, nuclear pores


nuclear envelope is a double membrane system made of an outer and an inner membrane. Also called nuclear membrane.




nuclear pores are holes in the nuclear envelope where things can pass into and out of the nucleus. Transcription occurs in the nucleus, and those transcribed RNA need to pass out of the nucleus. Things like transcription factors need to pass into the nucleus where they can access the DNA to be transcribed.



Membrane-bound Organelles

Mitochondria


site of ATP production: an apparatus called the ATP synthase makes ATP from ADP by utilizing the proton gradient as the driving force. The proton gradient is where the proton H+ concentration is higher in the inter-membrane space than the matrix of the mitochondria.




self-replication; have own DNA and ribosomes.



mitochondria replicate independently from the cell containing the mitochondria.




mitochondria does not share the same genome with its host.




mitochondria has their own ribosomes, which are different from the host’s ribosomes in both sequence and structure.




All these serve to support the endosymbiosis theory.





inner and outer membrane



Inner membrane surrounds the matrix.




The folds of the inner membrane make up the cristae.




Between the outer and inner membrane is the intermembrane space.




The intermembrane space is high in protons H+.




The outer membrane separates the mitochondria from the cytoplasm.




Lysosomes (vesicle containing hydrolytic enzymes)


Digests things like food and viral/bacterial particles.




Things you want to digest gets into a vacuole by endocytosis or phagocytosis, and then the vacuole fuses with the lysosome. Anything inside gets digested by the hydrolytic enzymes.



Endoplasmic reticulum:


Rough (RER) and Smooth (SER)RER (site of ribosomes): the ribosomes attach to the outside of rough ER and synthesis protein into the lumen.



rough ER has ribosomes studded over it, smooth ERs don’t.




RER deals with protein synthesis, folding, modification, and export.




SER deals with biosynthesis of lipids and steroids, and metabolism of carbohydrates and drugs.




In the muscles, the SER or SR stores and regulates calcium.





role in membrane biosynthesis: SER (lipids), RER (transmembrane proteins)



SER = makes lipids of the plasma membrane.




RER = makes transmembrane proteins, carries them on its membrane, RER membrane forms vesicles and bud off, fuses with the plasma membrane, transmembrane proteins now on the plasma membrane.






RER (role in biosynthesis of transmembrane and secreted proteins that cotranslationally targeted to RER by signal sequence)All ERs have a double membrane and is connected to the nuclear membrane (an old aamc topic, no longer tested).



Transmembrane proteins, or proteins that are to be secreted (need RER vesicle) have a signal sequence right at the beginning.




When ribosome starts making those proteins, they make the signal sequence first.




Signal sequence recruits a signal recognition particle that drags it to the RER.




ribosome now on the RER continues making the protein, but snakes it into the lumen.




Signal sequence is clipped off.







Golgi apparatus (general structure; role in packaging, secretion, and modification of glycoprotein carbohydrates)



looks like stacks of pancakes.




modifies and/or secretes macromolecules for the cell.




RER make protein → modified in the Golgi → buds off golgi and secreted out of cell by exocytosis.




Glycoprotein = protein with attached saccharides.




Golgi can glycosylate proteins as well as modifying existing glycosylations.




Glycosylation affects protein’s structure, function, and protect it from degradation.



Plasma Membrane

General function in cell containment
Protein and lipid components, fluid mosaic model: the fluid mosaic model basically describes the membrane as protein boats floating in a sea of lipids.
Osmosis: water diffuses freely across the membrane, but not ions. So osmosis occurs readily.
Passive and active transport: things that can’t readily diffuse across the membrane are transported across the membrane either without energy (passive) or with energy (active).
Membrane channels: to help ions to cross the membrane, there are ion channels.
*Sodium-potassium pump: 3 sodium (NA+) out, 2 potassium (K+) in. Thus, the cell maintains a negative resting potential.
Membrane receptors, cell signaling pathways, second messengers


Many hormones can NOT cross the plasma membrane, so they bind to membrane receptors on the outside.




Receptor binding triggers the production of second messengers.




Second messengers cause a change inside the cell (through a protein kinase cascade).




Cell signaling pathways:



1. Contact signaling = physical contact triggers a change inside cell.




2. Chemical signaling = chemical binding to receptor triggers a change inside cell.



Nerves use neurotransmitters.




The endocrine system use hormones.





3. Electrical signaling = change in membrane potential triggers change in cell.



Action potential along neurons propagates and cause release of neurotransmitters into synapse..




Action potential along muscle cell membrane causes contraction.





Membrane potential: the resting potential of the cell membrane is negative because of the sodium-potassium pump.
Exocytosis and endocytosis: exo = getting stuff out, endo = taking stuff in.
Cell-cell communication (General concepts of cellular adhesion)


A. Gap Junctions: connects two cells, and allows stuff to flow through between the cells.




B. Tight Junctions: stitches/glues two cells together, and does not allow stuff to flow through between the cells. A series of cells with tight junctions also effectively forms an impermeable barrier.




C. Desmosomes: connects two cells together by linking their cytoskeleton. They are organized for mechanical strength, not an impermeable barrier.



Cytoskeleton


General function in cell support and movement
Microfilaments (composition; role in cleavage and contractility)


made of actin




responsible for cytokinesis. Supports cell shape by bearing tension.



Microtubules (composition; role in support and transport)


made of tubulin




responsible for mitotic spindle, cilila/flagella, intracellular transport of organelles and vesicles. Supports cell shape by bearing compression.



Intermediate filaments (role in support)
composition is varied.
supports cell shape by bearing tension.

Composition and function of eukaryotic cilia and flagella


made of microtubules (eukaryotic)




cilia can be for locomotion, sensory, or for sweeping mucus.




flagella is used for locomotion.



Centrioles, microtubule organizing centers. Microtubules radiate out of these barrel shaped structures, which are made of microtubules themselves.

Great Review of the Eukaryotic Cell! 

Nucleus

  • Defining characteristics (membrane bound nucleus, presence of organelles, mitotic division)
  • Defining characteristics = what sets eukaryotes apart from prokaryotes.
  • Eukaryotes have a true nucleus (membrane-bound), while prokaryotes don’t.
  • Eukaryotes have membrane-bound organelles (ER, Golgi, lysosomes, mitochondria), prokaryotes don’t.
  • Eukaryotes divide by mitosis (all them chromosomes line up and stuff), prokaryotes undergo binary fission (no chromosomes, just a circular ring of DNA, no need for complex mitosis)

  • Nucleus (compartmentalization, storage of genetic information)
    • compartmentalization: nuclear membrane / nuclear envelope surrounds the nucleus.
    • genetic information is stored inside the nucleus as DNA.
  • Nucleolus (location and function)
    • location is a region inside the nucleus.
    • function is to transcribe ribosomal RNA (rRNA).
  • Nuclear envelope, nuclear pores
    • nuclear envelope is a double membrane system made of an outer and an inner membrane. Also called nuclear membrane.
    • nuclear pores are holes in the nuclear envelope where things can pass into and out of the nucleus. Transcription occurs in the nucleus, and those transcribed RNA need to pass out of the nucleus. Things like transcription factors need to pass into the nucleus where they can access the DNA to be transcribed.

Membrane-bound Organelles

  • Mitochondria
    • site of ATP production: an apparatus called the ATP synthase makes ATP from ADP by utilizing the proton gradient as the driving force. The proton gradient is where the proton H+ concentration is higher in the inter-membrane space than the matrix of the mitochondria.
    • self-replication; have own DNA and ribosomes.
      • mitochondria replicate independently from the cell containing the mitochondria.
      • mitochondria does not share the same genome with its host.
      • mitochondria has their own ribosomes, which are different from the host’s ribosomes in both sequence and structure.
      • All these serve to support the endosymbiosis theory.
    • inner and outer membrane
      • Inner membrane surrounds the matrix.
      • The folds of the inner membrane make up the cristae.
      • Between the outer and inner membrane is the intermembrane space.
      • The intermembrane space is high in protons H+.
      • The outer membrane separates the mitochondria from the cytoplasm.
  • Lysosomes (vesicle containing hydrolytic enzymes)
    • Digests things like food and viral/bacterial particles.
    • Things you want to digest gets into a vacuole by endocytosis or phagocytosis, and then the vacuole fuses with the lysosome. Anything inside gets digested by the hydrolytic enzymes.
  • Endoplasmic reticulum:
    • Rough (RER) and Smooth (SER)RER (site of ribosomes): the ribosomes attach to the outside of rough ER and synthesis protein into the lumen.
      • rough ER has ribosomes studded over it, smooth ERs don’t.
      • RER deals with protein synthesis, folding, modification, and export.
      • SER deals with biosynthesis of lipids and steroids, and metabolism of carbohydrates and drugs.
      • In the muscles, the SER or SR stores and regulates calcium.
    • role in membrane biosynthesis: SER (lipids), RER (transmembrane proteins)
      • SER = makes lipids of the plasma membrane.
      • RER = makes transmembrane proteins, carries them on its membrane, RER membrane forms vesicles and bud off, fuses with the plasma membrane, transmembrane proteins now on the plasma membrane.
    • RER (role in biosynthesis of transmembrane and secreted proteins that cotranslationally targeted to RER by signal sequence)All ERs have a double membrane and is connected to the nuclear membrane (an old aamc topic, no longer tested).
      • Transmembrane proteins, or proteins that are to be secreted (need RER vesicle) have a signal sequence right at the beginning.
      • When ribosome starts making those proteins, they make the signal sequence first.
      • Signal sequence recruits a signal recognition particle that drags it to the RER.
      • ribosome now on the RER continues making the protein, but snakes it into the lumen.
      • Signal sequence is clipped off.
  • Golgi apparatus (general structure; role in packaging, secretion, and modification of glycoprotein carbohydrates)
    • looks like stacks of pancakes.
    • modifies and/or secretes macromolecules for the cell.
    • RER make protein → modified in the Golgi → buds off golgi and secreted out of cell by exocytosis.
    • Glycoprotein = protein with attached saccharides.
    • Golgi can glycosylate proteins as well as modifying existing glycosylations.
    • Glycosylation affects protein’s structure, function, and protect it from degradation.

Plasma Membrane

  • General function in cell containment
  • Protein and lipid components, fluid mosaic model: the fluid mosaic model basically describes the membrane as protein boats floating in a sea of lipids.
  • Osmosis: water diffuses freely across the membrane, but not ions. So osmosis occurs readily.
  • Passive and active transport: things that can’t readily diffuse across the membrane are transported across the membrane either without energy (passive) or with energy (active).
  • Membrane channels: to help ions to cross the membrane, there are ion channels.
  • *Sodium-potassium pump: 3 sodium (NA+) out, 2 potassium (K+) in. Thus, the cell maintains a negative resting potential.
  • Membrane receptors, cell signaling pathways, second messengers
    • Many hormones can NOT cross the plasma membrane, so they bind to membrane receptors on the outside.
    • Receptor binding triggers the production of second messengers.
    • Second messengers cause a change inside the cell (through a protein kinase cascade).
    • Cell signaling pathways:
      • 1. Contact signaling = physical contact triggers a change inside cell.
      • 2. Chemical signaling = chemical binding to receptor triggers a change inside cell.
        • Nerves use neurotransmitters.
        • The endocrine system use hormones.
      • 3. Electrical signaling = change in membrane potential triggers change in cell.
        • Action potential along neurons propagates and cause release of neurotransmitters into synapse..
        • Action potential along muscle cell membrane causes contraction.
  • Membrane potential: the resting potential of the cell membrane is negative because of the sodium-potassium pump.
  • Exocytosis and endocytosis: exo = getting stuff out, endo = taking stuff in.
  • Cell-cell communication (General concepts of cellular adhesion)
    • A. Gap Junctions: connects two cells, and allows stuff to flow through between the cells.
    • B. Tight Junctions: stitches/glues two cells together, and does not allow stuff to flow through between the cells. A series of cells with tight junctions also effectively forms an impermeable barrier.
    • C. Desmosomes: connects two cells together by linking their cytoskeleton. They are organized for mechanical strength, not an impermeable barrier.

Cytoskeleton

  • General function in cell support and movement
  • Microfilaments (composition; role in cleavage and contractility)
    • made of actin
    • responsible for cytokinesis. Supports cell shape by bearing tension.
  • Microtubules (composition; role in support and transport)
    • made of tubulin
    • responsible for mitotic spindle, cilila/flagella, intracellular transport of organelles and vesicles. Supports cell shape by bearing compression.
  • Intermediate filaments (role in support)
    • composition is varied.
    • supports cell shape by bearing tension.
  • Composition and function of eukaryotic cilia and flagella
    • made of microtubules (eukaryotic)
    • cilia can be for locomotion, sensory, or for sweeping mucus.
    • flagella is used for locomotion.
  • Centrioles, microtubule organizing centers. Microtubules radiate out of these barrel shaped structures, which are made of microtubules themselves.
  • 25th April
    2014
  • 25
Great Immunology Videos 
Immunology Overview 
Innate Immune System
Adaptive Immune System 
Immune Cell Map 1 - Immune Cells 
Immune Cell Map 2 - Organs and Tissues
Immune Cell Map 3 - T cells part 1
Immune Cell Map 4 - T cells part 2

For More Great video review click Here! he has great reviews on all systems and subject needed for MCAT Biology Section!
And Check my Archive for my Previous review! 

Great Immunology Videos 

Immunology Overview 

Innate Immune System

Adaptive Immune System 

Immune Cell Map 1 - Immune Cells 

Immune Cell Map 2 - Organs and Tissues

Immune Cell Map 3 - T cells part 1

Immune Cell Map 4 - T cells part 2

For More Great video review click Here! he has great reviews on all systems and subject needed for MCAT Biology Section!

And Check my Archive for my Previous review! 

  • 9th April
    2014
  • 09
Today I almost died …
I got in a really bad accident on my motor bike and despite wearing a helmet and leather I am still missing various parts of flesh. I would also be missing half my face if it wasn’t for my helmet. Please always wear a helmet and make sure your friends and patients do as well. It’s much cooler to wear appropriate gear then be covered in scar tissue bc you didn’t!
  • 7th April
    2014
  • 07
The road to medicine is by no means an easy path, but nor is anything in life. When you find what your passionate about, there is nothing you’ll work as hard to achieve. So remember when your piled in books or can’t get any sleep because your running endless rounds. There is nothing out there that would be as happy working as hard for! There is nothing greater than knowing you’ve made a difference in someone’s life for the better :)

Always remember: Where’s a Will, there’s a Way!

The road to medicine is by no means an easy path, but nor is anything in life. When you find what your passionate about, there is nothing you’ll work as hard to achieve. So remember when your piled in books or can’t get any sleep because your running endless rounds. There is nothing out there that would be as happy working as hard for! There is nothing greater than knowing you’ve made a difference in someone’s life for the better :) Always remember: Where’s a Will, there’s a Way!

  • 31st March
    2014
  • 31
That awesome moment when you finish writing your honors thesis!!!

But then you have your thesis defense…

And your just like….

but outside when you walk in for your defense your like …

And you begin your thesis like …

when your committee questions your results during your defense ….

when its finished, you walk out like …

 

when you realize its finally over …

and then your like!!! …

fin. 

  • 31st March
    2014
  • 31
I’ve gotten a lot of questions from people about when they should take the MCAT. If you are planning to Apply in May(registration opens), don’t take it any later than mid-April! This way you can get your MCAT score back before you submit your application in June. This is important because you don’t want to apply until you have/know your MCAT scores. If you don’t do as well as you expected then you can take it again or wait to apply next year. Additionally Medical schools will NOT look at your application until you give them an MCAT score, if you say you are gonna retake it, the will NOT look at your application until you send them the new score!!!!! So please plan out when to take you MCAT with enough time to retake it (hopefully you won’t have to) before application submission in June. I would recommend taking it in the summer and not doing anything else during this time if possible. Study for the MCAT while taking classes or working full time will not fair well for most people, unless you are one of those epically awesome people who does super well on standardized tests. Remember to start studying AT LEAST 3 months before your scheduled deadline! If you don’t feel ready for the MCAT, move your test date back, its cheaper to move it than to pay to take it all over again! 

I’ve gotten a lot of questions from people about when they should take the MCAT. If you are planning to Apply in May(registration opens), don’t take it any later than mid-April! This way you can get your MCAT score back before you submit your application in June. This is important because you don’t want to apply until you have/know your MCAT scores. If you don’t do as well as you expected then you can take it again or wait to apply next year. Additionally Medical schools will NOT look at your application until you give them an MCAT score, if you say you are gonna retake it, the will NOT look at your application until you send them the new score!!!!! So please plan out when to take you MCAT with enough time to retake it (hopefully you won’t have to) before application submission in June. I would recommend taking it in the summer and not doing anything else during this time if possible. Study for the MCAT while taking classes or working full time will not fair well for most people, unless you are one of those epically awesome people who does super well on standardized tests. Remember to start studying AT LEAST 3 months before your scheduled deadline! If you don’t feel ready for the MCAT, move your test date back, its cheaper to move it than to pay to take it all over again! 

  • 31st March
    2014
  • 31
MCAT MATH REVIEW!!! 
- I know it sound terrible for some one you but I really recommend taking Calculus for the MCAT, It really helps a lot!
Remember Ladies and Gents: NO Calculator on the MCAT so get use to doing simple math in your head and memorizing some rules and the required math stuff you need to know (look at my archive for previous post about required math to know!)
1. FREERICE.ORG - every problem you get right they donate 10 grains of rice to the World Food Programme to help end hunger! Also good for testing basic skills in chemistry and other categories for the MCAT
2. MCAT THINKING: Fast Math Skills & Techniques - MCAT focused Math review and tricks 
3. Video Math Review! Good review of trick with triangles for physics section
4. Most Comprehensive Math Review for MCAT!!! This is an epic PDF full of awesomeness, pretty much all the math you will need to know for the whole MCAT!!! 
5. Practice! 

MCAT MATH REVIEW!!! 

- I know it sound terrible for some one you but I really recommend taking Calculus for the MCAT, It really helps a lot!

Remember Ladies and Gents: NO Calculator on the MCAT so get use to doing simple math in your head and memorizing some rules and the required math stuff you need to know (look at my archive for previous post about required math to know!)

1. FREERICE.ORG - every problem you get right they donate 10 grains of rice to the World Food Programme to help end hunger! Also good for testing basic skills in chemistry and other categories for the MCAT

2. MCAT THINKING: Fast Math Skills & Techniques - MCAT focused Math review and tricks 

3. Video Math Review! Good review of trick with triangles for physics section

4. Most Comprehensive Math Review for MCAT!!! This is an epic PDF full of awesomeness, pretty much all the math you will need to know for the whole MCAT!!! 

5. Practice! 

  • 31st March
    2014
  • 31
  • 23rd March
    2014
  • 23
  • 21st March
    2014
  • 21
This book is an awesome review of Genetics! With lots of awesome fun pictures, if you didn’t get to take Genetics for the MCAT or if it is one of your week spots, I definitely recommend this fun and awesome book as a good review source! Plus its by one of my favorites, beatricebiologist 
Description:
A crash course in genetics!
Everyone knows that if you come from a family of brunettes, you’re likely to be born with brown hair. But did you know your hair color may also affect how often you get sunburned? Or how often you need to take vitamin supplements?
What’s in Your Genes? goes beyond Gregor Mendel and dominant/recessive genes to show you all the ins and outs of what determines your DNA. Each entry provides you with a sneak peek into your DNA sequence and teaches you exactly how your body is able to create that wonderful you-ness that no one else has. From your tastebuds to your eye color to your obsession with clinical-strength deodorants, this book not only guides you through the history and study of genetics, but also shows you how those four little letters in your DNA make you who you are.
Complete with imaginative illustrations, What’s in Your Genes? reveals all there is to know about heredity—like the science behind vibrant red hair, perfect teeth, and your ability to see in color.
You can get her book here or are Barnes & Noble! 

This book is an awesome review of Genetics! With lots of awesome fun pictures, if you didn’t get to take Genetics for the MCAT or if it is one of your week spots, I definitely recommend this fun and awesome book as a good review source! Plus its by one of my favorites, beatricebiologist 

Description:

A crash course in genetics!

Everyone knows that if you come from a family of brunettes, you’re likely to be born with brown hair. But did you know your hair color may also affect how often you get sunburned? Or how often you need to take vitamin supplements?

What’s in Your Genes? goes beyond Gregor Mendel and dominant/recessive genes to show you all the ins and outs of what determines your DNA. Each entry provides you with a sneak peek into your DNA sequence and teaches you exactly how your body is able to create that wonderful you-ness that no one else has. From your tastebuds to your eye color to your obsession with clinical-strength deodorants, this book not only guides you through the history and study of genetics, but also shows you how those four little letters in your DNA make you who you are.

Complete with imaginative illustrations, What’s in Your Genes? reveals all there is to know about heredity—like the science behind vibrant red hair, perfect teeth, and your ability to see in color.

You can get her book here or are Barnes & Noble! 

  • 21st March
    2014
  • 21
Coagulation, Clotting Mechanisms, Role of Liver in production of Clotting Factors
SUMMARY - Clotting is a + Positive Feedback Mechanism + Clotting, leads to MORE (not less) clotting. Platelets are sticky pieces of megakaryoctyes, they contain enzymes for clotting. Clotting factors are produced in the Liver (Fibrinogen), which then circulates in the blood plasma. When a wound occurs, the platelets pile up onto it (platelet plug) and release chemicals that activate the fibrinogen. The fibrinogen follows are series of reactions becoming —> fibrin (a mesh that seals the clot during coagulation). Retraction and repair occur as the clot contracts (the clot dissolves after the wounded blood vessel is repaired).
Platelets contain enzymes and chemicals needed involved in the clotting process.
Liver produces clotting factors (eg. fibrinogen), which circulates in blood plasma.
Coagulation = liquid blood → gel
- Clotting Mechanism - 


1. Platelet plug formation: wound + platelets → platelets clump at wound, release chemicals, activates clotting factors.




2. Coagulation: series of clotting factor/enzyme activation that ends in fibrinogen → fibrin. Fibrin being the fiber mesh that seals the clot.




3. Retraction and repair: clot contracts, gets compact, but after the wounded blood vessel repairs itself, the clot dissolves.


For a more comprehensive review click here! 
For a video on this, click me!
And to test your knowledge on the subject, clickity click! 
photo complements to: larstheyeti

Coagulation, Clotting Mechanisms, Role of Liver in production of Clotting Factors

SUMMARY - Clotting is a + Positive Feedback Mechanism + Clotting, leads to MORE (not less) clotting. Platelets are sticky pieces of megakaryoctyes, they contain enzymes for clotting. Clotting factors are produced in the Liver (Fibrinogen), which then circulates in the blood plasma. When a wound occurs, the platelets pile up onto it (platelet plug) and release chemicals that activate the fibrinogen. The fibrinogen follows are series of reactions becoming —> fibrin (a mesh that seals the clot during coagulation). Retraction and repair occur as the clot contracts (the clot dissolves after the wounded blood vessel is repaired).

  • Platelets contain enzymes and chemicals needed involved in the clotting process.
  • Liver produces clotting factors (eg. fibrinogen), which circulates in blood plasma.
  • Coagulation = liquid blood → gel

  • - Clotting Mechanism - 
  • 1. Platelet plug formation: wound + platelets → platelets clump at wound, release chemicals, activates clotting factors.
  • 2. Coagulation: series of clotting factor/enzyme activation that ends in fibrinogen → fibrin. Fibrin being the fiber mesh that seals the clot.
  • 3. Retraction and repair: clot contracts, gets compact, but after the wounded blood vessel repairs itself, the clot dissolves.


For a more comprehensive review click here! 

For a video on this, click me!

And to test your knowledge on the subject, clickity click

photo complements to: larstheyeti

  • 12th March
    2014
  • 12

Transcription of DNA into RNA, enzymatic reactions, RNA, RNA degradation

  • Transcription
    1. Initiation: promoter recognition, closed complex, open complex.
      • Promoter:
        • Prokaryotic: ←upstream, -35 region, Pribnow box, transcription start site (TSS, +1), downstream→
        • Eukaryotic: ←upstream, several upstream elements, TATA box, initiator element containing TSS (+1), downstream→
        • The high A-T composition in promoters facilitate unwinding of DNA.
        • Template strand = antisense strand = (-) strand = noncoding strand = the DNA strand that serves as the template for transcription.
        • Nontemplate strand = sense strand = (+) strand = coding strand = the DNA strand having the same sequence as the transcribed RNA.
      • Binding to promoter:
        • Prokaryotic:
          • holoenzyme = core enzyme (polymerase activity) + σ-subunit (promoter and strand specificity).
          • binding first forms the closed complex, and then DNA opens up, forms the open complex.
        • Eukaryotic:
          • A whole bunch of transcription factors (TFs) involved in promoter recognition, binding, and openning up DNA.
          • TBP = Tata binding protein. TAF = TBP associated factor.
          • Phosphorylation of Pol II C-terminal domain (CTD) opens DNA up, forms the open complex.
        • Polymerase must transcribe using the correct template strand. The σ-factor (prokaryotes) and TFs (eukaryotes) tell the RNA polymerase to bind the coding strand, while using the template strand as the template.
    2. Elongation:
      • Polymerases:
        • Prokaryotes have just one.
        • Eukaryotes have three:
          • 1. RNA Pol I: makes rRNA (except the small 5S rRNA that resembles a tRNA in size).
          • 2. RNA Pol II: makes mRNA.
          • 3. RNA Pol III: makes tRNA (and 5S rRNA).
      • Incorporation of NTPs.
      • Prokaryotes lose σ-subunit. Eukaryotes lose TFs.
      • Topoisomerases relaxing supercoils ahead and behind the polymerase.
      • Transcription-coupled repair: RNA Pol II encounters DNA damage, backs up, TFIIH comes along, recruits repair enzymes. Defective TFIIH → faulty transcription-coupled repair → Xeroderma pigmentosum and Cockayne syndrome (skin sensitive to sunlight radiation in both diseases).
    3. Termination
      • Prokaryotic:
        • Intrinsic termination: GC hairpin (stalls polymerase) followed by poly U (slips off).
        • Rho-dependent termination: ρ protein catches up to polymerase when it stalls at the hairpin, and bumps it off.
      • Eukaryotic:
        • Termination consensus sequence reached (AAUAAA).
        • Polymerase released somewhere further downstream to the consensus sequence.
  • RNA
    • 1. RNA = ribonucleic acid, has 2’-OH.
    • 2. rRNA = ribosomal RNA
      • Most abundant (r for rampant).
      • Catalyzes peptide bond formation in the ribosome.
    • 3. mRNA = messenger RNA
      • Longest (m for massive).
      • Contains sequence of codons for translation.
      • RNA splicing
        • pre-mRNA need to be processed.
        • Introns = interfering sequences, cut out.
        • Exons = spliced together.
        • RNA splicing proceeds via a lariat intermediate, by the action of the spliceosome (snRNPs), introns released in lariat form.
        • Some RNA can self splice.
    • 4. tRNA = transfer RNA
      • Smallest (t for tiny).
      • Contains anticodon.
      • Shuttles the correct amino acid to the correct codon during translation.
    • 5. snRNPs (snurps) = RNA + protein, involved in RNA splicing.
  • RNA degradation
    • RNases degrade RNA.
    • Post-transcriptional modifications protect RNA from degradation (5’ cap and polyA tail)
    • 2’-O-methylation prevents that position from attacking the RNA backbone.