Translation: Amino acids and exceptions to the genetic code (concept map)

Map summary:

Codons on mRNA pair with anti-codons on TRNA

Genetic code is redundant ( 64 different codons for 20 amino acids)

Redundancy protects from mutation (in principle)

Exceptions to the genetic code: Mitochondria and protists have different start and stop codon identities,

Lastly there are the two nonstandard amino acids which are used via transnational recoding and are not a part of the genetic code itself.

Functional organization of the cardiovascular system (concept map)

Map summary:

We have division of labor where parts of the carviovascular system are separated but connected both via pressure inputs and outputs but also in terms of biological processes. Because of this connectivity, pathologies in one area of the cardiovascular system can be observed in other areas such as is the case where pulmonary edema is observed in congestive heart failure and tracheal deviation is observed in pulmonary emboli.

The parallel arterial system enables blood flow from one organ system to have no effect on another (thanks to the fractality of your blood network and impedance matching).

The major exception to this is the hepatic portal vein which drains GI and other splanchic organs to the liver and then the inferior vena cava. Going off the earlier point of connectivity, patients with hepatitis frequently present with ascites.

This map also contains details about the generic vessel structure and vasodilation and vasoconstriction: note the differences in receptor types .

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RNAi: Differences and similarities between siRNA vs miRNA and RITS vs RISC (Concept map)

Map summary:

MicroRNAs are:

  1. Endogenous to our genome (conserved genes)
  2. act on many types of mRNA’s and possibly other RNA’s
  3. act primarily in plant and animal development

SiRNAs are:

  1. of viral origin
  2. only act on ONE type of mRNA

both are cut into a functional molecule via DICER protein

When said cuts are combined with other proteins to form a complex they are EITHER

  1. RITS: (RNA induced transcriptional silencing)
  2. RISC: (RNA induced silencing complex)

RITS acts to epigeneitcally modify chromatin

RISC acts to either block translation or degrade the mRNA

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Cardiomyocyte calcium regulation (load independent inotropy: positive and negative inotropes concept map)

Inotropy is basically a fancy scientific word for how strong or weak a contraction is, in this case in we are discussing inotropy regulation that is INDEPENDENT of loading.

Since action potentials (movement of sodium and potassium) are “all or nothing” phenomenon. When it comes to regulating inotropy at the cellular level it mostly revolves around calcium regulation. Which works via three main pathways: ligand interactions, voltage gated confirmational changes, and active transport mechanisms that control how much calcium is in the cell.


PKA acts on Troponin 1 and Phospholambon. The latter to inhibit or activate Calcium ATPases at the sarcoplasmic reticulum and the former to influence the stability of myosin and actin interactions via changes in Troponin 1’s calcium affinity. L-Type DHPs are voltage gated calcium channels on the sarcoplasmic reticlulum. Finally we have Primary and Secondary active transport controlling the overall movement of calcium in and out of the cell along with the movement of calcium in and out of the sarcoplasmic reticulum.

For further reference material in understanding the concept map above here are some videos:

Amino Acid Catabolism

Biochemistry is basically a very complicated story of how carbon chains can be reduced, aminated, oxidized, and etc to make you.

Today’s concept map is on Amino Acid Catabolism.

Step 1. Removal of the Amino group.

This is accomplished via Aminotransferases followed up with oxidative Deamination, and then by tossing the NH4 group into the Urea Cycle.

Step 2. Metabolize the carbon chains

There are two types of pathways for this: Glucogenic and Ketogenic.

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