Biochemistry, an offshoot of biology and Chemistry, studies the chemical substances and processes within living organisms. Biochemistry holds great significance across areas of research and medicine.
Biochemistry Assignmеnt Hеlp offеrs a grеat hеlp in undеrstanding thе concеpts of biochemistry. Not only that we also help Australian students with thе other branchеs of biological science.
Biochеmistry is a Lab sciеncе that еxplorеs chеmistry rеlatеd to living organisms. Biochеmists do study thе structurе, composition, and chеmical reactions of substancеs in living systеms, thеir functions, and ways to control thеm.
Thе Topics covеrеd in Biochеmistry includе:
Aerobic Respiration provides energy to the vast majority of organisms on this planet earth. Even Plants rely on aerobic respiration to lead their life. Respiration as we all know is the process of breaking down complex food substances into simpler food substances, accompanied by the release of energy, captured in compounds known as ATP (Adenosine triphosphate).
Glycolysis, also known as the Embden-Meyerhoff-Parnas pathway is the very first metabolic pathway in both aerobic organisms and anaerobic organisms. Aerobes after this follow Oxidative decarboxylation, Kreb’s cycle and ETS (Oxidative Phosphorylation).
Anaerobes after glycolysis follow fermentation or phosphorylation (other than oxygen as terminal acceptor).
Overview of Glycolysis:
Glycolysis is the conversion of Glucose to Pyruvate in a series of steps and harnessing the energy released, into ATP at every possible step.
Glycolysis is a 10-step reaction that can be divided into two phases. Phase 1: Energy Investment Phase and Phase 2: Energy Recovery Phase.
In the investment phase of every Glycolysis reaction, 2 ATPs are invested into one molecule. But in the recovery phase, the recovery of ATP will be made from two molecules.
Step 1: Hexokinase phosphorylates Glucose at the 6th position in the presence of ions, to make it Glucose-6-phosphate. (One ATP investment). This step locks the glucose inside the cell to metabolise it completely.
Step 2: Phosphoglucose isomerase (PGI) isomerises Glucose-6-phosphate to fructose-6-phosphate. This step ensures symmetry in Step 4.
Step 3: Phosphofructokinase (PFK) phosphorylates Frusctose-6-phosphate at 1st position in the presence of ions, to make it into fructose-1,6-bisphosphate.
Step 4: Fructose-1,6-bisphosphate generated in the above step is broken down by aldolase into two 3-carbon compounds as Glyceraldehyde-3-phosphate (G-3P) and Dihydroxyacetone phosphate (DHAP).
Step 5: G-3-P can only be burnt. Therefore, DHAP formed in step 4 is isomerised to G-3-P. This step is catalysed by Triose Phosphate Isomerase. With this step, we have to phosphate molecules on two 3-carbon compounds.
Step 6: G-3-P is the first high-energy intermediate, aldehyde. The hydrogen in G-3-P is harvested as NADH (a high-energy compound, which can be later transformed into ATP, One NADH is equivalent to 3 ATP) in the presence of the catalyst Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH). This step converts G-3-P into 1,3-bisphospoglycerate (1,3-BPG).
From two G-3-P molecules, 2-NADH are generated.
Step 7: This step releases the phosphate. 1,3-BPG is converted into 3-phosphoglycerate (3-PG) catalysed by Phosphoglycerate Kinase (PGK). The released phosphate is captured into ATP.
From two 1,3-BPG, 2 ATP are yielded.
Step 8: 3 - PG is converted to 2-Phosphoglycerate (2-PG) catalysed by Phosphoglycerate mutase (PGM). A mutase transfers the functional group from one position to the other.
Step 9: This step forms the second high-energy intermediate PEP. 2-PG is dehydrated into Phosphoenolpyruvate (PEP).
Step 10: The enzyme Pyruvate Kinase generates the ATP from PEP, converting PEP into Pyruvate.
From two PEP molecules, 2 ATP are yielded.
Thus, in glycolysis, we invested a total of 2 ATP in one 6-carbon molecule, which yielded a total of 4 ATP in the recovery phase (see steps 7 and 10). The net yield is 2 ATP.
Steps 7 and 10 are referred to as Substrate Level Phosphorylation, as these reactions yield ATP at the substrate level and don’t require an Electron Transport chain to yield ATP.
Pyruvate formed in the above step undergoes either of the three fates.
The amount of energy released in the above processes can be summed up as
Aerobic Respiration > Anaerobic Respiration > Fermentation.
Regulation of Glycolysis:
Glycolysis is a stepwise reaction in which each step is associated with the release of Energy. From the laws of thermodynamics, we call that energy “Free Energy”.
The reactions of Glycolysis are represented by a waterfall diagram, where the vertical line represents the changes associated with free energy. The larger the line the more is the irreversibility. Therefore, 1, 3 and 10 are the irreversible steps of Glycolysis, the other being in near equilibrium, are reversible.
The rate of metabolism depends on the three enzymes Hexokinase, Phosphofructokinase (PFK) and Pyruvate Kinase of 1, 3 and 10 respectively. These enzymes are the candidates of Flux-control (Glycolysis flow). A typical human cell has many ways to control these enzymes. PFK is the most studied step of all three.
ATP is the inhibitory substrate for the above enzymes, as more ATP is indicative of the excess amount of Energy available.
ADP (Adenosine diphosphate) and AMP (Adenosine Monophosphate) reverse the inhibitory effects.
There is still another way through which Glycolysis can be regulated, Substrate cycling. In substrate cycling the near equilibrium steps 2, 4, 6, 8, and 9 are regulated. The near equilibrium steps proceed approximately with the same speed, in both directions, which dictates the constant flow of the glycolytic flux in normal conditions.
When there is a demand for a large amount of energy, then the enzyme that catalyses the reverse step is inhibited so that the flux proceeds in the forward direction favouring the formation of pyruvate in large amounts.
Structure of DNA:
DNA is Deoxyribose Nucleic acid. DNA is a polymer of Nucleotides.
A nucleotide has Nitrogen Base, a pentose Sugar, and a phosphorous group.
A nucleotide is named with respect to the pentose sugar.
The pentose sugar in DNA is deoxyribose (2nd carbon has a “-H” group). The nitrogen base is attached to the first (1 prime) carbon of the pentose sugar. The phosphate group is attached to the fifth (5 prime) carbon of the pentose sugar. The third (3 prime) position of pentose sugar is the -OH group.
The nitrogen bases are Adenine (A), Thymine (T), Cytosine (C) and Guanine (G). Adenine and Guanine resemble Purine rings and are referred to as Purines. Thymine and Cytosine resemble Pyrimidine rings and are referred to as Pyrimidines.
The rule in DNA pairing is that a purine always pairs with a pyrimidine, however, Adenine pairs only with Thymine and Guanine pairs only with Cytosine, and vice versa.
Rule in forming a polymer of DNA:
The rule in forming the polymer of DNA is that the 5 prime of pentose sugar pairs with the 3 prime of the next pentose. This bond is referred to as a “Phosphodiester Bond”. This generates a free 5 prime phosphate group at one end and a free 3 prime OH at the other end.
The backbone of a DNA strand is phosphor diester bonds and the pentose sugars, whereas the nitrogen bases are puckered inside the chain.
Structure of DNA:
The structure of DNA at physiological pH is a right-handed double helix, in which the two polymers of DNA run in antiparallel directions. If one strand is 5 prime to 3 prime, then the other strand will be 3 prime to 5 prime.
The nitrogen bases are puckered inside the DNA molecule, in which we see A and T double bonded, whereas G and C triple bonded. The nitrogen bases lie perpendicular to the pentose phosphate backbone.
The other key feature of DNA (B-form) is that it has a pitch (one complete turn) of 3.4 nm, and the distance between two bases in a polymer is 0.34 nm. In complete turn, there will be 10 nucleotides found in a polymerised strand of DNA.The diameter (width) of the DNA or the distance between two base pairs is 2.0 nm.
The structure here discussed is only of a primary level. There are many levels in the packaging of DNA.
This double helical structure is attributed to the hydrophobic nature of the Nitrogen bases. The hydrophilic portion of pentose phosphate chains, therefore, lie oriented towards the cytoplasmic environment.
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