thelifeofapremed

thelifeofapremed:

The Official Guide to the MCAT Exam says to know the graphical representations of these dependences …

@ = Proportional

1) y @ x
2) y @ -x
3) y @ sqrt x
4) y @ 1/x
5) y @ 1 x^2
6) y @ sin x
7) y @ cos x

All of theses ^ are in the beautiful dance moves picture of above so practice these dance moves and MCAT graphs won’t stand a chance ;)

proportional (Linear)
inversely proportional (slow curve)
exponential (fast Curve)
Ect.

thelifeofapremed

thelifeofapremed:

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.
thelifeofapremed
thelifeofapremed:

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.

thelifeofapremed:

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.