Biyokimya/Metabolizma ve enerji

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Metabolizma[değiştir]

Anabolizma ve katabolizma[değiştir]

Metabolizma (Şekil 1) yaygın tabirle besinin enerjiye, hücre yapılarına ve atık ürünlere dönüşümüdür.

Biochemistry metabolism 1.png
Şekil 1: Metabolizmaya genel bakış

Yukarıdaki diyagram metabolizmanın farklı parçalarını göstermektedir:

  • enerji kaynağı, her şeyden önce, enerjisi fotosentez yoluyla kullanılan güneştir.
  • katabolizma, besinin kimyasal enerjiye yıkımıdır.
  • anabolizma, küçük çevresel moleküllerden kimyasal enerjiyi kullanarak karmaşık hücresel moleküllerin üretimidir.

Katabolik tepkimeler enerji açığa çıkartır, bu yüzden egzergonik (enerji veren)tir; fakat anabolik epkimeler enerjiyi tüketirler ve bu yüzden endergonik (enerji alan)tir.

Yüksek enerjili fosfatlar[değiştir]

Besin bileşenlerinin çok çeşitli olması ve anabolizmada enerjiye ihtiyaç duyan biyokimyasal tepkime sayısının fazla olması sebebiyle belirli bir anabolik tepkimeyi, katabolizmadaki belirli bir enerji kaynağıyla eşleştirmek oldukça yetersiz olacaktır. Onun yerine hücre, bir ara bileşik, bir çeşit evrensel enerji birimi kullanır. Bu ara madde yüksek enerjili fosfat olarak adlandırılır.

Ancak bir fosfat rubu ne zaman "yüksek enerjili" olur, "düşük enerjili" fosfatla aralarındaki fark nedir? Açığa çıkan şey hidrolizin ΔG0'sidir. Hidroliz bir bileşikten su ekleyerek fosfatı ayırır:

   O                      O
R-OP-OH + H2O ⇌ R-OH + HO-P-OH
   O                      O

Düşük enerjili (inorganik) fosfatın ΔG0''ı (Pi olarak adlandırılır) 9-20 kJ mol-1'dir, fakat yüksek enerjili fosfatın (Ⓟ ile gösterilir) ΔG0''ı ~30 kJ mol-1'dir.

pKa değeri[değiştir]

Ⓟ'ı bu kadar özel yapan şey nedir? Bunu açıklamak için, pH ve pKa değerlerininin ne olduğuna bakmalıyız. Bir fosfat grubu sıfırla üç arasında OH grubuna sahiptir. Bu da Ⓟ'a, içinde bulunduğu çözeltinin pH grubuna bağlı olarak dört farklı formda (0, 1, 2 ve 3 OH grubu içeren, Şekil 2) bulunma olanağı verir. pKa değeri ise moleküllerin yarısı bir formda (mesela bir OH grubu içeren) diğer yarısı da başka bir formda (mesela 2 OH grubu içeren) ikenki pH değeridir. Bu Henderson-Hasselbalch eşitliği ile ifade edilir:

Biochemistry metabolism 2.png
Şekil 2: Bir fosfat grubunun dört formu pKa2 hücre içindeki koşulları temsil eder.

Now to the promised difference between Ⓟ and PPi. The breaking of the ester bond of an ROⓅ releases more energy than the breaking of a PPi bond (Fig. 3), because of

  1. electrostatic repulsion between the two phosphate groups in PPi
  2. resonance stabilization of two Pi groups, compared to PPi (Fig. 4)

Biochemistry metabolism 3.png
Figure 3: Hydrolysis of Ⓟ and PPi.

Biochemistry metabolism 4.png
Figure 4: Resonance stabilization of Pi.

Resonance stabilization means that both OH and =O can "travel" around the phosphate. Of course, this is a crude analogy; they do not really move, the electrons are just "smeared" around the phosphate atom. This is also indicated by the use of the ↔ arrow, instead of ⇌; the three forms do not exist, they are just a way of writing down the chemical reality.

As you can see in Fig. 3, the ΔG0' value for PPi⇌2Pi is ≪0, shifting the reaction strongly in favor of the 2Pi.

Molecules using high-energy phosphates[değiştir]

Anhydride between phosphoric acid and carboxyl group[değiştir]

Hydrolysis : ΔG0' = -49.3 kJ mol-1
Biochemistry metabolism 5a.png

Guanidine phosphate[değiştir]

Hydrolysis : ΔG0' = -43.0 kJ mol-1
Biochemistry metabolism 5b.png

Enol phosphate[değiştir]

For example, phosphoenolpyruvate
Hydrolysis : ΔG0' = -61.9 kJ mol-1
Biochemistry metabolism 5c.png

ATP[değiştir]

Adenosine triphosphate contains one low-energy and two high-energy phosphate bonds:
Biochemistry metabolism 5d.png
Low energy : ΔG0' = -14,2 kJ mol-1
High energy : ΔG0' = -30.5 kJ mol-1

  • ATP is regenerated from ADP (adenosine diphosphate), Pi and energy (from food); H2O is released in the process.
  • ATP is the short-term energy "currency" of the cell.
  • ATP concentration in the cell is low (ATP: 2-8mM; ADP:0,2-0,8mM). ATP is generated in high "turn over".
  • ATP performs its chemical work through coupled reactions.
  • Coupled reactions are always Ⓟ transfers, never direct hydrolysis

Basically, any ATP-driven reaction is reversible, building ATP from ADP and Pi in the process. However, some ATP-driven reactions should never be reversed; these include nucleotide and protein synthesis. If these were reversed, the organism would disassemble its own DNA and proteins for energy, a rather unfortunate strategy. For reactions that should never be reversed, ATP can be broken down into AMP (adenosine monophosphate) and PPi, which in turn becomes 2×Pi. This reaction has a ΔG0' of -65,7 kJ mol-1, which is totally irreversible under in vivo conditions.

It should be noted that AMP can not directly be converted to ATP again. Instead, the enzyme AMP kinase forms two ADP molecules from one ATP and one AMP. The resulting ADPs are then treated as described above.

Non-covalent bonds[değiştir]

The destruction of covalent bonds takes up huge amounts of energy. The breakdown of an O2 molecule into two oxygen atoms needs ~460 kJ mol-1. Thus, nowhere in "living" biochemistry are covalent bonds actually destroyed; if one is broken, another one is created. Nonetheless, many biochemical functions are using so-called weak/secondary/non-covalent bonds.

Weak bonds are created and destroyed much more easily than covalent ones. The typical range of energy needed to destroy such a weak bond is 4-30 kJ mol-1. Thus, the formation of weak bonds is energetically favorable, but these bonds are also easily broken by kinetic (thermal) energy (the normal movement of molecules). Biochemical interactions are often temporary (e.g., a substrate has to leave an enzyme quickly after being processed), for which the weakness of these bonds is essential. Also, biochemical specificity (e.g., enzyme-substrate-recognition) is achieved through weak bonds, utilizing two of their major properties:

  • Since individual weak bonds are, well, weak, several of them have to occur in a specific pattern at the same time in roughly the same place.
  • The short range of weak bonds.

There are three basic types of weak bonds, and a fourth "pseudo-bond":

Ionic bonds[değiştir]

Ionic bonds are electrostatic attractions between permanently charged groups. Ionic bonds are not directed. Example:

X-CO2- ..... H3+N-Y
~ 20 kJ mol-1

Hydrogen bonds[değiştir]

Hydrogen bonds are also established by electrostatic attraction, though not between permanently charged groups, but rather between atoms temporarily charged by a dipole moment, resulting from the different electronegativity of atoms within a group. Hydrogen bonds are even weaker than ionic bonds, and they are highly directional, usually along a straight line. The most common hydrogen bonds in biochemistry are:

X-OH ..... O-Y
X-OH ..... N-Y
X-NH ..... O-Y
X-NH ..... N-Y

Hydrogen bonds equal an energy between 12-29 kJ mol-1.

Van der Waals attractions[değiştir]

Van der Waals attractions are established between electron density-induced dipoles. They form when the outer electron shells of two atoms almost (but not quite) touch. The distance of the atoms is very important for these weak interactions. If the atoms are too far apart, the interactions are too weak to establish; if the atoms are too close to each other, their electron shells will repel each other. Van der Waals attractions are highly unspecific; they can occur between virtually any two atoms. Their energy is between 4-8 kJ mol-1. [[File:Example.jpgŞablon:Subject]]

Hydrophobic forces[değiştir]

Hydrophobic forces are not actually bonds, so this list has four items, but still just three bond types. In a way hydrophobic forces are the negation of the hydrogen bonds of a polar solute, usually water, enclosing a nonpolar molecule. For a polar solute like water, it is energetically unfavorable to "waste" a possible hydrogen bond by exposing it towards a nonpolar molecule. Thus, water will arrange itself around any nonpolar molecule in such a way that no hydrogen bonds point towards that molecule. This results in a higher order, compared to "freely" moving water, which leads to a lower entropy level and is thus energetically unfavorable. If there is more than one nonpolar molecule in the solute, it is favorable for the nonpolar molecules to aggregate in one place, reducing their surrounding, ordered "shell" of water to a minimal surface. Also, in large molecules, such as proteins, the hydrophobic (nonpolar) parts of the molecule will tend to turn towards the inside, while the polar parts will tend to turn towards the surface of the molecule.