Nucleotides and Nucleic Acids WTH are they

What Are Organic Molecules?

Organic molecules contain carbon-hydrogen bonds, are found in living things and can be very large molecules. The major classes of organic macromolecules are  carbohydrates, proteins, lipids and nucleic acids.

 What Are Nucleotides really?

Nucleotides are monomers (small molecules) that are the building blocks of nucleic acids. Each nucleotide, and consists of 3 portions:

-a pentose sugar called ribose

-one or more phosphate groups

-one of five cyclic nitrogenous bases

Some nucleotides are put together to form nucleic acid (DNA & RNA) macromolecules, whereas others function on their own. ​

Nucleic Acid Structure

Nucleotides can be linked together by covalent bonds between the phosphate of one nucleotide and the sugar of next. These linked monomers become the phosphate-sugar backbone of nucleic acids. The nitrogenous bases extend out from this phosphate-sugar backbone like teeth of a comb.

Deoxyribonucleic Acid (DNA)

DNA (deoxyribonucleic acid) is the genetic material, the original blueprint, inside each biological cell. The molecule is double-stranded and twisted, like a spiral staircase, with the two sugar-phosphate chains as the side rails, and the nitrogenous base pairs, linked by hydrogen bonds, forming the rungs. In addition to linking the bases together, hydrogen bonding twists the phosphate-sugar backbones into a helix, thus DNA is a double helix.There are four different types of nitrogenous bases that can be found in a DNA molecule: adenine (A), guanine (G), cytosine (C) and thymine (T). Adenine and guanine are larger, double ring nitrogenous bases called purines. Cytosine and thymine are smaller, single ring nitrogenous bases called pyrimidines. When bases pair up between the two DNA strands, a purine always pairs with a pyrimidine. Specifically adenine (A) and thymine (T) pair up, and cytosine (C) and guanine (G) pair up. These bases are attracted to each other through hydrogen bonding.When the DNA molecule is inactive, the bases are linked by these hydrogen bonds and the molecule is in its spiral-shaped state. When DNA is being used—either being copied (a process called replication) or being employed to build proteins (involving the processes of transcription and translation)—the DNA molecule must be opened up, essentially “unzipped” between the bases.

Ribonucleic Acids (RNA)

In living organisms, RNA is a single stranded nucleic acid molecule. In viruses, non-living infectious particles, RNA can be single or double stranded.There are four different types of nitrogenous bases found in an RNA molecule: adenine (A), guanine (G), cytosine (C) and uracil (U). In RNA, uracil takes the place of the thymine found in DNA.

When RNA bases are laid down to build an RNA molecule, DNA is unzipped, and the new RNA molecule made is compliment of the DNA template. For example, if the DNA strand has the following bases, in this order, ATTGCACT, the new RNA molecule being made will have the base sequence UAACGTGA. After the RNA segment is made, the DNA zips back up and the RNA floats off to carry out its function in the cell.Genetic information copied from DNA is used to build three types of RNA:

1) Ribosomal RNA – The Protein Factories: Most of the RNA in cells is part of the structure of small cellular organelles known as ribosomes, the protein factories of the cells.

2) Messenger RNA – The Genetic Blueprint: Messenger RNA is a copy of the genetic information that was transcribed from the cell’s original blueprint, DNA. This copy of the genetic information is brought to the ribosome and used as instructions for building proteins.

3) Transfer RNA – The Amino Acid Suppliers: Transfer RNA is also part of the process of building proteins. Like a little truck, tRNA brings the amino acid to the ribosome. Which amino acid it brings depends on which was coded for in the mRNA instructions. At the ribosome, these amino acids are joined together to form proteins.

ATP: The Energy Transfer Molecule

Adenosine 5′-triphosphate (ATP) is a multifunctional nucleotide, most important as the “molecular currency” of intracellular energy transfer. Like tiny rechargeable batteries, ATP molecules transport chemical energy within a biological cell. These molecules can move energy around because the phosphate bonds contain a lot of potential energy, which is released when they are broken.During photosynthesis and cellular respiration, ATP is produced from ADP (adenosine diphosphate), an inorganic phosphate and added energy. ATP energy is consumed by a multitude of cellular processes.

 

So how was my presentation:

reference:

“What are Nucleotides and Nucleic Acids,” Science Prof Online; accessed on April 13, 2013.http://www.scienceprofonline.org/chemistry/nucleotides-nucleic-acids-atp-rna-dna.html

Lactose VS Alcohol fermentation

Reference;http://www.methuen.k12.ma.us/mnmelan/chpt9-17.jpg

The Citric Acid Cycle Is Controlled at Several Points

The rate of the citric acid cycle is precisely adjusted to meet an animal cell’s needs for ATP.The primary control points are the allosteric enzymes isocitrate dehydrogenase and α-ketoglutarate dehydrogenase

Control of the Citric Acid Cycle. The citric acid cycle is regulated primarily by the concentration of ATP and NADH. The key control points are the enzymes isocitrate dehydrogenase and α-ketoglutarate dehydrogenase.

Isocitrate dehydrogenase is allosterically stimulated by ADP, which enhances the enzyme’s affinity for substrates. The binding of isocitrate, NAD⁺, Mg²⁺, and ADP is mutually cooperative. In contrast, NADH inhibits iso-citrate dehydrogenase by directly displacing NAD⁺. ATP, too, is inhibitory. It is important to note that several steps in the cycle require NAD⁺ or FAD, which are abundant only when the energy charge is low.

A second control site in the citric acid cycle is α-ketoglutarate dehydrogenase. Some aspects of this enzyme’s control are like those of the pyruvate dehydrogenase complex, as might be expected from the homology of the two enzymes. α-Ketoglutarate dehydrogenase is inhibited by succinyl CoA and NADH, the products of the reaction that it catalyzes. In addition, α-ketoglutarate dehydrogenase is inhibited by a high energy charge. Thus, the rate of the cycle is reduced when the cell has a high level of ATP.

In many bacteria, the funneling of two-carbon fragments into the cycle also is controlled. The synthesis of citrate from oxaloacetate and acetyl CoA carbon units is an important control point in these organisms. ATP is an allosteric inhibitor of citrate synthase. The effect of ATP is to increase the value of K_M for acetyl CoA. Thus, as the level of ATP increases, less of this enzyme is saturated with acetyl CoA and so less citrate is formed.

reference: “The Citric Acid cycle is Controlled at Several Points,” NCBI, assessed on April 10,  2013, http://www.ncbi.nlm.nih.gov/books/NBK22347/.

 

Points noted on glycolysis:

 

-Hexokinase takes the terminal from ATP to add to glucose-6-phosphate

-Every cell has glucose transporters. By phosphorylating glucose-6 phosphate, the glucose cannot move but by adding phosphate to glucose, it becomes unstable (abit) and activated which promotes reaction.

-Phosphofructokinase-1 is the most regulated enzyme followed by hexokinase in glycolysis.

-Bisphosphate has 2 phosphates not attached to the same carbon as in diphosphate.

-Aldolase does the splitting where G3P and DP are isomers of each other.

-DHAP does not contiune in glycolysis.

-TPI converts DHAP to G3P so you get 2 molecules of G3P at the end of the prep-phase.

-TPI is a kinetically perfect enzyme.

-All kinases require Mg2+ as a cofactor because it stabilizes the charge on the ATP molecule.

-All enzymes have an induced fit to prevent water from hydrolysing ATP.

-Oxidation phase in the pay-off section is energetically feasible.

-Oxidation provides energy to phosphates to form 1-3-BPG(2) amd would be unfeasible without oxidation.

-Gylcolysis cannot go on without NAD+ (low conc. in cells)

-3ways to get ATP: substrate-level phosphorylation, oxidative phosphorylation and photo-phosphorylation in plants.

-1-3 BP is a very high energy molecule.

-Most ATP comes form Oxidative phosphorylation.

 

reference:

David L. Nelson, Michael M. Cox. Lehninger Principles of Biochemistry. New York: W. H.

Freeman and Company, 2008.

Glycolysis at its best

Glycolysis at its best

An interactive way of developing your glyco-skills