Capacitor

CAPACITOR
Capacitor is an electronic device, which is used to store electric charge or electrical energy. A capacitor     stores electric charge on its plates. There are a number of types of capacitors available.
STRUCTURE OF CAPACITOR
A capacitor consists of two identical conducting plates which are placed in front of each other. One          plate of capacitor is connected to the positive terminal of power supply and the other plate is connected     to negative terminal. The plate, which is connected to positive terminal acquired positive charge, and the     other plate connected to negative terminal. Separation between the plates in very small. The space     between the plates is field with air or any suitable dielectric material
A parallel plate capacitor
PRINCIPLE OF CAPACITOR
Electric charge stored between the plates of a capacitor is directly proportional to the potential     difference between the plates.
Let the potential difference between the plates is V and the charge stored on any one of the plates of     capacitor is Q then,
Q a V Q = CV
where     C= Capacitance of the capacitor
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CAPACITANCE
Charge storing capability of a capacitor is called capacitance of capacitor.     Definition: Capacitance of a capacitor is defined as the ratio of the charge stored on any of the plates of     capacitor to the potential between the plates.
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Mendel's Law of Independent Assortment

Mendel's Law of Independent Assortment

To this point we have followed the expression of only one gene. Mendel also performed crosses in which he followed the segregation of two genes. These experiments formed the basis of his discovery of his second law, the law of independent assortment. First, a few terms are presented.

Dihybrid cross - a cross between two parents that differ by two pairs of alleles (AABB x aabb)

Dihybrid- an individual heterozygous for two pairs of alleles (AaBb)

Again a dihybrid cross is not a cross between two dihybrids. Now, let's look at a dihybrid cross that Mendel performed.

Parental Cross: Yellow, Round Seed x Green, Wrinkled Seed

F₁ Generation: All yellow, round

F₂ Generation: 9 Yellow, Round, 3 Yellow, Wrinkled, 3 Green, Round, 1 Green, Wrinkled

At this point, let's diagram the cross using specific gene symbols.

Choose Symbol	Seed Color: Yellow = G; Green = g
	Seed Shape: Round = W; Wrinkled = w

The dominance relationship between alleles for each trait was already known to Mendel when he made this cross. The purpose of the dihybrid cross was to determine if any relationship existed between different allelic pairs.

Let's now look at the cross using our gene symbols.

Now set up the Punnett Square for the F₂ cross.

		Female Gametes
		GW	Gw	gW	gw
	GW	GGWW (Yellow, round)	GGWw (Yellow, round)	GgWW (Yellow, round)	GgWw (Yellow, round)
Male	Gw	GGWw (Yellow, round)	GGww (Yellow, wrinkled)	GgWw (Yellow, round)	Ggww (Yellow, wrinkled)
Gametes	gW	GgWW (Yellow, round)	GgWw (Yellow, round)	ggWW (Green, round)	ggWw (Green,
	gw	GgWw (Yellow, round)	Ggww (Yellow, wrinkled)	ggWw (Green, round)	ggww (Green, wrinkled)

The phenotypes and general genotypes from this cross can be represented in the following manner:

Phenotype	General Genotype
9 Yellow, Round Seed	G_W_
3 Yellow, Wrinkled Seed	G_ww
3 Green, Round Seed	ggW_
1 Green, Wrinkled Seed	ggww

The results of this experiment led Mendel to formulate his second law.

Mendel's Second Law - the law of independent assortment; during gamete formation the segregation of the alleles of one allelic pair is independent of the segregation of the alleles of another allelic pair

As with the monohybrid crosses, Mendel confirmed the results of his second law by performing a backcross - F₁dihybrid x recessive parent.

Let's use the example of the yellow, round seeded F₁.

Punnett Square for the Backcross

		Female Gametes
		GW	Gw	gW	gw
Male Gametes	gw	GgWw (Yellow, round)	Ggww (Yellow, wrinkled)	ggWw (Green, round)	ggww (Green, wrinkled)

The phenotypic ratio of the test cross is:

• 1 Yellow, Round Seed
• 1 Yellow, Wrinkled Seed
• 1 Green, Round Seed
• 1 Green, Wrinkled Seed

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Development Of Chick

Stages in chick embryo development

One of the greatest miracles of nature is the transformation of the egg into the chick. A chick emerges after a brief three weeks of incubation. The complexity of the development cannot be understood without training in embryology.

When the egg is laid, some embryonic development has occurred and usually stops until proper cell environmental conditions are established for incubation to resume. At first, all the cells are alike, but as the embryo develops, cell differences are observed. Some cells may become vital organs; others become a wing or leg.

Soon after incubation begins, a pointed thickened layer of cells becomes visible in the caudal or tail end of the embryo. This pointed area is the primitive streak, and is the longitudinal axis of the embryo. From the primitive streak, the head and backbone of the embryo develop. A precursor of the digestive tract forms; blood islands appear and will develop later into the vascular or blood system; and the eye begins.

On the second day of incubation, the blood islands begin linking and form a vascular system, while the heart is being formed elsewhere. By the 44^th hour of incubation, the heart and vascular systems join, and the heart begins beating. Two distinct circulatory systems are established, an embryonic system for the embryo and a vitelline system extending into the egg.

At the end of the third day of incubation, the beak begins developing and limb buds for the wings and legs are seen. Torsion and flexion continue through the fourth day. The chick's entire body turns 90^o and lies down with its left side on the yolk. The head and tail come close together so the embryo forms a "C" shape. The mouth, tongue, and nasal pits develop as parts of the digestive and respiratory systems. The heart continues to enlarge even though it has not been enclosed within the body. It is seen beating if the egg is opened carefully. The other internal organs continue to develop. By the end of the fourth day of incubation, the embryo has all organs needed to sustain life after hatching, and most of the embryo's parts can be identified. The chick embryo cannot, however, be distinguished from that of mammals.

The embryo grows and develops rapidly. By the seventh day, digits appear on the wings and feet, the heart is completely enclosed in the thoracic cavity, and the embryo looks more like a bird. After the tenth day of incubation, feathers and feather tracts are visible, and the beak hardens. On the fourteenth day, the claws are forming and the embryo is moving into position for hatching. After twenty days, the chick is in the hatching position, the beak has pierced the air cell, and pulmonary respiration has begun.

After 21 days of incubation, the chick finally begins its escape from the shell. The chick begins by pushing its beak through the air cell. The allantois, which has served as its lungs, begins to dry up as the chick uses its own lungs. The chick continues to push its head outward. The sharp horny structure on the upper beak (egg tooth) and the muscle on the back of the neck help cut the shell. The chick rests, changes position, and keeps cutting until its head falls free of the opened shell. It then kicks free of the bottom portion of the shell. The chick is exhausted and rests while the navel openings heal and its down dries. Gradually, it regains strength and walks. The incubation and hatching is complete. The horny cap will fall off the beak within days after the chick hatches.

EVENTS IN EMBRYONIC DEVELOPMENT

Before Egg Laying:

Fertilization
Division and growth of living cells
Segregation of cells into groups of special function (tissues) 

Between Laying and Incubation

No growth; stage of inactive embryonic life

During Incubation: 

First day

16 hours - first sign of resemblance to a chick embryo
18 hours - appearance of alimentary tract
20 hours - appearance of vertebral column
21 hours - beginning of nervous system
22 hours - beginning of head
24 hours - beginning of eye

Second day

25 hours - beginning of heart
35 hours - beginning of ear
42 hours - heart beats

Third day

60 hours - beginning of nose
62 hours - beginning of legs
64 hours - beginning of wings

Fourth day - beginning of tongue
Fifth day - formation of reproductive organs and differentiation of sex
Sixth day - beginning of beak
Eighth day - beginning of feathers
Tenth day - beginning of hardening of beak
Thirteenth day - appearance of scales and claws
Fourteenth day - embryo gets into position suitable for breaking shell
Sixteenth day - scales, claws and beak becoming firm and horny
Seventeenth day - beak turns toward air cell
Nineteenth day - yolk sac begins to enter body cavity
Twentieth day - yolk sac completely drawn into body cavity; embryo occupies practically all the space within the egg except the air cell
Twenty-first day - hatching of chick

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Dominance

One of Gregor Mendel's great discoveries was the Principle of Dominance. He noted that when he hybridized two parents with different versions of a particular trait, one of those versions apparently disappeared in the hybrid (heterozygous) offspring. If he then mated those offspring to each other, the vanished trait reappeared in the third generation, apparently completely unchanged despite being invisible in generation 2. He named the version of the trait which was visible in the hybrids the dominant and the one that was invisible in the hybrids the recessive.
We now know that Mendel discovered complete dominance, which is only one of several different kinds of dominance relationships. Dominance relationships result from the interactions of the gene products of different alleles of the same gene (not from interactions between different genes). Note that dominance is virtually always defined with respect to the phenotypic of the heterozygote.

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Complete Dominance: If two alleles have a complete dominance relationship, the phenotype of the heterozygote will be indistinguishable from the phenotype of the homozygous dominant. For example, for one of the gerbil fur color genes, that wild type agouti/brown allele (B) is completely dominant to the black (b) allele of the same gene. BB gerbils are brown; bb gerbils are black; Bb gerbils are brown. And you can't tell by looking at a brown gerbil whether it is BB or Bb, no matter how closely or carefully you look.
Incomplete Dominance: If two alleles have an incomplete dominance relationship, the phenotype of the heterozygote will be intermediate between the phenotypes of the two homozygotes. This is often described as "blending," though the alleles themselves do not blend. The phenotype of looks like the two traits have blended together. For example, in snapdragons, one of the various genes which control flower color has two alleles, one for red flowers and one for white flowers. The two homozygous plants will produce red and white flowers, respectively. But the heterozygote will produce pink flowers--as if the two homozygous conditions were blended together like paint. In this case, the actual flower color (phenotype) probably results from varying amounts of production of the red pigment. The homozygous red plant produces a lot of the pigment, the homozygous white plant produces none of the pigment, and the heterozygote produces half as much as the homozygous red. Note that there is no dominant allele here.
Codominance: Codominance is similar to incomplete dominance in that there is no dominant allele. However, the phenotypic expression is quite different. If two alleles have a codominance relationships, in the heterozygote both alleles will be completely expressed. For example, in humand ABO blood types, two of the three alleles (the A allele, properly designated as I^A, and the B allele, properly designated as I^B) are codominant. This gene controls the deposition of antigenic markers on cells. A person with blood type A (homozygous for I^A or heterozygous for I^A and the recessive i (for O type)) has one kind of antigen marker, while a person with blood type B (homozygous for I^B or heterozygous for I^B and the recessive i (for O type)) has a slightly different kind of antigen marker. The heterozygote has blood type AB, and this person's cells have both A antigens and B antigens on their surfaces. There is no "in-between" antigen, as would be expected if the alleles showed incomplete dominance. Both of the alleles are completely expressed, and the person has both blood types at the same time.
Pseudodominance: In some cases, the relationship between two alleles appears to be one of complete dominance, but actually isn't. Clues that a dominance relationship is one of complete dominance would be that there are only two phenotypes for that trait (as in the brown/black example above, vs the red/pink/white result from incomplete dominance), and that when you make a monohybrid cross (mate heterozygote to heterozygote) your results give you quite a few more offspring with the "dominant" trait than with the "recessive" trait, and that one of your phenotypes would be able to "hide" alleles for the other phenotype. Note that in our example of complete dominance above, the heterozygous brown gerbils were hiding the presence of their recessive black alleles. These alleles could be discovered only by breeding to see if the black color would be revealed in offspring. So how could two alleles have these characteristics but not have complete dominance? The answer is that there are cases in which one of your possible allelic combinations is lethal--that an offspring which inherits this particular combination dies during development.
For example, in fruit flies there is a gene called "curly." There are two phenotypes for this gene--the normal, straight winged flies, and flies whose wings curl upward. Straight winged flies can't give birth to curly winged flies, but if you mate two curly winged flies, some of their offspring will be straight winged. And they will always have more curly offspring than straight offspring. This all sounds exactly like complete dominance, with curly being dominant to straight. But if you examine the results from the curly x curly mating more closely, they actually don't meet expecations for complete dominance. When you perform a monohybrid cross for a gene with complete dominance, your offspring numbers will fit the "3 dominant:1 recessive" phenotypic ratio. Curly x curly gives a 2 curly:1 straight phenotypic ratio. This is very odd all by itself, as genetics is very much a binary business; it just shouldn't give ratios that add up to three; they should all add up to some multiple of two.
The explanation for this oddity is that curly is not really dominant to straight. Homozygous curly flies never hatch out of their eggs. For reasons which are unknown, homozygotes for this allele always die before hatching, and are thus never counted among the living offspring. The genotypic ratio from this mating is exactly what you expect it to be: 1 curly-curly:2 curly-straight:1 straight-straight. But the curly-curly flies all die, so the living offspring are 2 curly-straight:1 straight-straight, and thus the 2 curly:1 straight phenotypic ratio. If this were truly complete dominance, the curly-straight flies would have the same phenotype as the curly-curly flies (see above). But the phenotype of the curly-curly flies is "dead."

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Dominance, of course, is all about phenotype. And a lot more goes into shaping the final phenotype than just dominance. Phenomena like variable penetrance, variable expressivity and epistasis all impact on how genes are expressed. No gene exists or functions in a vacuum; all of them operate in a cellular and organismal environment created by and influenced by all of the other genes in the organism. In addition, many traits, such as the fur color and flower color traits used above as examples, are actually impacted upon by more than one gene. And, of course, there is always the external environment to be considered as well.

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Kreb's Cycle

Organisms derive the majority of their energy from the Kreb's Cycle, also known as the TCA cycle. The Kreb's Cycle is an aerobic process consisting of eight definite steps. In order to enter the Kreb's Cycle pyruvate must first be converted into Acetyl-CoA by pyruvate dehydrogenase complex found in the mitochondria.

Introduction

In the presence of oxygen organisms are capable of using the Kreb's Cycle. The reason oxygen is required is because the NADH and [FADH2] produced in the Kreb's Cycle are able to be oxydized in the electron transport chain (ETC) thus replenishing the supply of NAD+ and [FAD].

    

Steps

In order for pyruvate from glycolysis to enter the Kreb's Cycle it must first be converted into acetyl-CoA by the pyruvate dehydrogenase complex which is an oxidative process wherein NADH and CO2 are formed.  Another source of acetyl-CoA is beta oxidation of fatty acids.

1. Acetyl-CoA enters teh Kreb Cycle when it is joined to oxaloacetate by citrate synthase to produce citrate. This process requires the input of water. Oxaloacetate is the final metabolite of the Kreb Cycle and it joins again to start the cycle over again, hence the name Kreb's Cycle. This is known as the committed step
2. Citrate is then converted into isocitrate by the enzyme aconitase. This is accomplished by the removal and addition of water to yield an isomer.
3. Isocitrate is converted into alpha-ketogluterate by isocitrate dehydrogenase. The byproducts of which are NADH and CO2.
4. Apha-ketogluterate is then converted into succynl-CoA by alpha-ketogluterate dehydrogenase. NADH and CO2 are once again produced.
5. Succynl-CoA is then converted into succinate by succynl-CoA synthetase which yields one ATP per succynl-CoA.
6. Succinate coverts into fumerate by way of the enzyme succinate dehydrogenase and [FAD] is reduced to [FADH2] which is a prosthetic group of succinate dehydrogenase. Succinate dehydrogenase is a direct part of the ETC.  It is also known as electron carrier II.
7. Fumerate is then converted to malate by hydration with the use of fumerase. 
8. Malate is converted into oxaloacetate by malate dehydrogenase the byproducts of which are NADH.

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Protien Synthesis

As with any of the polymerization reactions, protein synthesis can be divided into three phases:
Initiation

where a functionally competent ribosome is assembled in the correct place on an mRNA ready to commence protein synthesis.

Elongation

whereby the correct amino acid is brought to the ribosome, is joined to the nascent polypeptide chain, and the entire assembly moves one position along the mRNA.

Termination

which happens when a stop codon is reached, there is no amino acid to be incorporated and the entire assembly dissociates to release the newly-synthesized polypeptide.

There are two rules about protein synthesis to keep in mind:

• mRNA is translated 5' -> 3'
  
• Proteins are synthesized from the N-terminus to the C-terminus

This account describes the steps of protein synthesis in bacteria; we will mention eukaryotic protein synthesis briefly at the end.

Initiation

This phase of protein synthesis results in the assembly of a functionally competent ribosome in which an mRNA has been positioned correctly so that its start codon is positioned in the P(peptidyl) site and is paired with the initiator tRNA.
The following ingredients are needed for this phase of protein synthesis:

• Two ribosome subunits - 30S and 50S
  
• The mRNA
  
• Three Initiation Factors - IF1, IF2 (GTP) and IF3
  
• The initiator fMet-tRNA_f^Met.

The following steps take place:
Binding of the ribosome 30S subunit with Initiation Factors

IF3 promotes the dissociation of the ribosome into its two component subunits. The presence of IF3 permits the assembly of the initiation complex and prevents binding opf the 50Ssubunit prematurely.
IF1 assists IF3 in some way, perhaps by increasing the dissociation rate of the 30S and 50S subunits of the ribosome.

Binding of tthe mRNA and the fMet-tRNAfMet

IF3 assists the mRNA to bind with the 30S subunit of the ribosome so that the start codon is correctly positioned at the peptidyl site of the ribosome. The mRNA is positioned by means of base-pairing between the 3' end of the 16S rRNA with the Shine-Dalgarno sequence immediately upstream of the start codon.
IF2(GTP) assists the fMet-tRNA_f^Met to bind to the 30S subunit in the correct site - the P site.
It is not clear whether the mRNA or fMet-tRNA_f^Met binds first. It may be that either can bind first.
At this stage of assembly, the 30S initiation complex is complete and IF3 can dissociate.

Binding of the ribosome 50S subunit and release of Initiation Factors

As IF3 is released, the 50S subunit of the ribosome binds to complete the initiation complex. Simultaneously, GTP hydrolysis occurs on IF2. This hydrolysis may be helped by the L7/L12 ribosomal proteins rather than by IF2 itself. Hydrolysis is required for dissociation of IF2. GTP hydrolysis probably serves as a timing mechanism to ensure that the tRNA is correctly positioned before IF3 dissociates.
Once IF2 and IF1 are both released, translation can proceed.

Elongation

Three special Elongation Factors are required for this phase of protein synthesis: EF-Tu (GTP), EF-Ts and EF-G (GTP).
The Elongation phase of protein synthesis consists of a cyclic process whereby a new aminoacyl-tRNA is positioned in the ribosome, the amino acid is transferred to the C-terminus of the growing polypeptide chain, and the the whole assembly moves one position along the ribosome:
Binding of a new aminoacyl-tRNA at the A site

At the start of each cycle, the A (aminoacyl) site on the ribosome is empty, the P (peptidyl) site contains a peptidyl-tRNA, and the E (exit) site contains an uncharged tRNA.
The elongation factor, EF-Tu (GTP) binds with an aminoacyl-tRNA and brings it to the ribosome. Once the correct aminoacyl-tRNA is positioned in the ribosome, GTP is hydrolyzed and EF-Tu (GDP) dissociates away from the ribosome.
There are two ways that EF-Tu functions to ensure that the correct aminoacyl-tRNA is in place:

• EF-Tu prevents the aminoacyl end of the charged tRNA from entering the A site on the ribosome. This ensures that codon-anticodon pairing is checked first before the charged tRNA is irreversibly bound in the A site and a new, potentially incorrect, peptide bond is made.
  
• GTP hydrolysis is SLOW and EF-Tu cannot dissociate from the ribosome until it occurs. The amount of time prior to GTP hydrolysis allows the final fidelity check to take place.
  
  If the anticodon-codon interaction is incorrect, the aminoacyl-tRNA simply dissociates and a new one is brought in. This check, however, can verify nothing about the aminoacid -- it simply verifies that the correct pairing takes place.
  
  
  Experiments using GTP analogues have been used to establish these results:
  
  • If a GTP analogue such as GTP-g-S, which is hydrolyzed very slowly, is used then protein synthesis slows down because of the slow rate of hydrolysis but it also becomes more accurate because there is more time to check that the correct aminoacyl-tRNA is in place.
    
  • If a GTP analogue such as GMP-PCP, which contains a non-hydrolyzable methylene bridge between the b and g phosphates, is used then protein synthesis stops because EF-Tu cannot dissociate from the ribosome.

EF-Tu is the most abundant protein in the E. coli cell. There are approximately 70-100,000 molecules/cell which is 5% of the total cell protein. There are also approximately 70-100,000 tRNA molecules/cell. Nearly all of the aminoacyl-tRNA in the cell is bound by EF-Tu.
EF-Tu cannot bind with tRNA_f^Met. This tRNA has a slight difference in its structure compared with that of tRNA^Met which means that it is not bound by EF-Tu.
EF-Tu (GDP) is inactive and cannot function to bind aminoacylated tRNAs. However, EF-Tu has a higher affinity for GDP (K_a = 10^-8M) than for GTP (K_a = 10^-6M).
In order to recycle EF-Tu, the elongation factor EF-Ts binds to the EF-Tu (GDP) complex to displace the GDP. GTP then, in turn, displaces EF-Ts. Many other G-proteins require a guanine nucleotide release protein (GNRP) to release GDP; EF-Ts is the GNRP for EF-Tu.

Formation of the new peptide bond (Transpeptidation)

Peptide bond formation occurs as a result of nucleophilic attack by the lone pair of electrons on the amino nitrogen of the aminoacyl-tRNA on the carbonyl carbon that attaches the growing polypeptide chain to a tRNA molecule in the P site of the ribosome. As a result, the peptide chain is attached to the tRNA which is paired with the codon in the A site. The new amino acid is, therefore, added to the C-terminal end of the polypeptide chain.
Older illustrations show this reaction as a transfer of the entire polypeptide chain from the tRNA in the P site to the tRNA in the A site. This is not an accurate representation. It is more likely that the aminoacyl arm of the tRNA in the A site extends to join with the polypeptide chain in the P site.
The peptidyltransferase activity of the ribosome which catalyzes this reaction is located on the 23S rRNA though it will be assisted by some of the ribosomal protein subunits. In other words, peptidyl transferase is a ribozyme - another example of a catalytic RNA.

Translocation of the Ribosome

Finally, the ribosome translocates along the mRNA thereby moving the new peptidyl-tRNA to the P site and the old (now uncharged) tRNA, which has just lost its peptidyl chain, to the E site. This step requires the elongation factor, EF-G(GTP). There are 20,000 molecules/cell of EF-G which is the same as the number of ribosomes.
GTP is hydrolyzed during translocation and, once again, GTP hydrolysis is required for dissociation of EF-G not for binding.
EF-G blocks the binding of aminoacyl tRNAs to the A site as well as blocking the binding of Release Factors. It effectively makes sure that translocation must take place before the cycle continues.
EF-G and the tRNA-EF-Tu complex are mutually exclusive. The structures of these two are remarkably similar and demonstrate very nicely why these two cannot bind to the ribosome simultaneously:

Phe-tRNA-EF-Tu	EF-G

The following diagram summarizes the movement of tRNA through the ribosome during the elongation phase of protein synthesis:

A new codon is now positioned at the A site and awaits a new aminoacyl-tRNA.

Termination

The final phase of protein synthesis requires that the finished polypeptide chain be detached from a tRNA. This can only happen in response to the signal that a stop codon has been reached. After hydrolysis, the ribosome subunits dissociate.
Binding of Release factors

There are no tRNAs that recognize the stop codons. Rather they are recognized by release factor RF1 (which recognizes the UAA and UAG stop codons) or RF2 (which recognizes the UAA and UGA stop codons). These release factors act at the A site of the ribosome. A third release factor, RF3 (GTP), stimulates the binding of RF1 and RF2.

Hydrolysis of the peptidyl-tRNA

Binding of the release factors alters the peptidyltransferase activity so that water is now the nucleophilic attack agent. The result is hydrolysis of the peptidyl-tRNA and release of the completed polypeptide chain. The uncharged tRNA then dissociates as do the release factors. GTP is hydrolyzed.

Dissociation

Finally, the ribosome dissociates into its 30S and 50S subunits and the mRNA is released. IF3 may help this process.

Antibiotics and Protein Synthesis

Many antibiotics and toxins funtion by blocking certain steps during protein synthesis. As well as their utility in treating infections, antibiotics have been useful in dissecting many of the molecular details of the steps and reactions of protein synthesis. The following will give you a feel for this important topic.

Chloramphenicol	Inhibits peptidyl transferase in prokaryotes. It binds near the L16 protein and seems to prevent the aminoacylated end of charged tRNAs from binding correctly to the A site on the ribosome.
Cycloheximide	Inhibits peptidyl transferase in eukaryotes.
Diphtheria Toxin	Inhibits the activity of EF-G byADP-ribiosylation.
Erythromycin	Blocks the translocation step of protein synthesis.
Fusidic Acid	Blocks the dissociation of eEF-2 during protein synthesis in eukaryotes.
Kanamycin	Causes misreading of the code by interfering with the wobble base pairing.
Kirromycin	Blocks dissociation of GDP from EF-Tu after hydrolysis. This prevents dissociation of EF-Tu from the ribosome and effectively stalls protein synthesis.
Puromycin	Causes premature chain termination. Its structure resembles that of the 3' end of a tyrosyl-tRNA and it participates as a substrate in a peptidyl transferase reaction. However, once it is added to the 3' end of a nascent protein, it does not provide a suitable centre for any further nucleophilic reactions, and protein synthesis is aborted.
Streptomycin	This antibiotic was the first aminoglycoside characterized. It inhibits prokaryotic ribosomes in a couple of ways. It causes misreading by interfering with the normal pairing between codon and anticodon. It can also prevent initiation. Streptomycin resistant bacteria carry an altered S12 subunit.
Tetracycline	Inhibits aminoacyl-tRNA binding to the A site on the ribosome.

Protein Synthesis in Eukaryotes

A major difference between eukaryotes and prokaryotes is that, in a typical eukaryotic cell, protein synthesis takes place in the cytoplasm while transcription and RNA processing take place in the nucleus. In bacteria, these two processes can be coupled so that protein synthesis can start even before transcription has finished.
The steps of protein synthesis are basically the same in eukaryotic cells as in prokaryotes. The ingredients, however, can be different -- we have already described some of them.

• Ribosomes are larger. 60S and 40S subunits combine to give 80S ribosomes. They contain 4 rRNAs: 28S, 5.8S and 5S in the 60S subunit; 18S in the 40S subunit.
  
• While the initiating amino acid in eukaryotic protein synthesis is still methionine, it is not formylated.
  
• Eukaryotic mRNA is capped. This is used as the recognition feature for ribosome binding -- not the 18S rRNA.
  
• The initiation phase of protein synthesis requires over 10 eukaryotic Initiation Factors (eIFs) one of which is the cap binding protein.
  
• The eukaryotic elongation phase closely resembles that in prokaryotes. The corresponding elongation factors are eEF-1a (EF-Tu), eEF-1bg (EF-Ts) and eEF-2 (EF-G).
• Eukaryotes require just a single release factor, eRF.

Coordinating Protein Synthesis with mRNA Synthesis

It has recently been found that the eukaryotic initiation factor eEF-4G binds not only with other factors in the initiation complex but also with PABP (polyA binding protein) which binds to the polyA tail of mRNA.


It is though that the binding of eEF-4G to PABP serves as a crticial recruitment step for driving downstream translation.
In another sense, however, the binding of eEF-4G to PABP represents a mechanism to ensure that only mature intact mRNAs are translated.

A similar problem arises in prokaryotes. Bacterial mRNA turns over much faster than eukaryotic mRNA and there is a much higher probability that the 3'-end of an mRNA will be degraded. If this happens, the consequences could be severe. If an mRNA has lost its stop codons, there will be no signals to promote dissociation of the ribosomes. Any ribosomes that have bound to a defective mRNA will therefore stall when they reach the broken end unable to continue and unable to dissociate efficiently.
E. coli (and other bacteria) has a mechanism to deal with this situation.
E. coli contains a small RNA, encoded by the ssrA gene, is synthesized as a 457 nt precursor RNA that is processed by RNaseE to a mature 363 nt RNA. This RNA is also known as tmRNA or 10Sa RNA.
The ssrA RNA has a number of important properties:

• Its secondary and tertiary structure partially resembles that of tRNA
  
• It can be charged with alanine
  
• It can be used as an mRNA which codes for a 10 amino acid long oligopeptide: ANDENYALAA. 

The mechanism of action of the ssrA RNA is shown in the following figure:


When a ribosome stalls, the ssrA RNA charged with alanine is brought to the A-site of the ribosome by the SsrB protein. Peptidyl transferase activity transfers the nascent polypeptide to the alanine attached to ssrA.
The mRNA template is also displaced by the ssrA RNA. Further protein synthesis now uses ssrA as a template and ten further amino acids (ANDENYALAA) are added to the C-terminal end of the polypeptide.
However, the final two amino acids that are added (AA) mark the new protein for proteolysis by the two proteases ClpAP and ClpXP.
Thus any proteins that are only partially synthesized by stalled ribosomes can be rapidly destroyed and turned over.

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Electron Transport Chain

The electron transport chain (aka ETC) is a process in which the NADH and [FADH2] produced during glycolysis, β-oxidation, and other catabolic processes are oxidized thus releasing energy in the form of ATP. The mechanism by which ATP is formed in the ETC is called chemiosmotic phosphorolation.

Introduction

The byproducts of most catabolic processes are NADH and [FADH2] which are the reduced forms. Metabolic processes use NADH and [FADH2] to transport electrons in the form of hydride ions (H-). These electrons are passed from NADH or [FADH2] to membrane bound electron carriers which are then passed on to other electron carriers until they are finally given to oxygen resulting in the production of water. As electrons are passed from one electron carrier to another hydrogen ions are transported into the intermembrane space at three specific points in the chain. The transportation of hydrogen ions creates a greater concentration of hydrogen ions in the intermembrane space than in the matrix which can then be used to drive ATP Synthase and produce ATP (a high energy molecule). 

Overview

In the diagram located below there are the major electron transporters responsible for making energy in the ETC.

The Electron Carriers

• I (NADH-ubiquinone oxidioreductase): An integral protein that receives electrons in the form of hydride ions from NADH and passes them on to ubiquinone
• II (Succinate-ubiquinone oxidioreductase aka succinate dehydrogenase from the TCA cycle): A peripheral protein that receives electrons from succinate (an intermediate metabolite of the TCA cycle) to yield fumarate and [FADH2]. From succinate the electrons are received by [FAD] (a prosthetic group of the protein) which then become [FADH2]. The electrons are then passed off to ubiquinone.
• Q (Ubiquinone/ ubiquinol): Ubiquinone (the oxidized form of the molecule) receives electrons from several different carriers; from I, II, Glycerol-3-phosphate dehydrogenase, and ETF. It is now the reduced form (ubiquinol) which passes its electron off to III.  
• III (Ubiquinol-cytochrome c oxidioreductase): An integral protein that receives electrons from ubiquinol which are then passed on to Cytochrome c
• IV (Cytochrome c oxidase):An integral protein that that receives electrons from Cytochrome c and transfers them to oxygen to produce water within the mitochondria matrix. 
• ATP Synthas: An integral protein consisting of several different subunits. This protein is directly responsible for the production of ATP via chemiosmotic phosphorolation. It uses the proton gradient created by several of the other carriers in the ETC to drive a mechanical rotor. The energy from that rotor is then used to phosphorolate ADT to ATP.

Not Shown

• ETF (Electron-transferring flavoprotein) Dehydrogenase: This peripheral protein located on the matrix side of the inner membrane is a part the B-oxidation cycle. Electrons from acyl-CoA are donated to an electron-transfer flavoprotien which are then transferred to ETF (Electron-transferring flavoprotein) Dehydrogenase in the form of [FADH2]. ETF dehydrogenase then passes those electrons from [FADH2] to ubiquinone and on through the ETC. 
• Glycerol-3-phosphate dehydrogenas:This peripheral protein located on the intermembrane space side of the inner membrane is a part of the glycerol-3-phosphate transport system. It accepts a proton from glycerol-3-phosphate to a prosthetic [FAD] group which yields [FADH2].  From [FADH2] the electrons are then given to ubiquinone and on through the ETC.  

Electron Flow

It should be noted from the diagram below that ubiquinone (a hydrophobic carrier that resides within the membrane) receives electrons from several different electron carriers. Cytochrome c (a hydrophilic carrier found with in the intermembrane space) on the other hand only transfers electrons from III to IV. The driving force of the ETC is the fact that each electron carrier has a higher standard reduction potential than the one that it accepts electrons from. Standard reduction potential is a measure of the ability to accept or donate electrons. Oxygen has the highest (most positive) standard reduction potential which means that is is most likely to accept electrons from other carriers. That is precisely why it is found at the end of the ETC.

Proton Motive Force

Proton motive force refers to the energy obtained from the proton gradient created by several of the electron carriers. Only three of the four mentioned electron carriers are capable of transporting protons from the matrix to the intermembrane space: I, III, and IV.  It is this proton gradient that drives phosphorolation of ADP to ATP as well as several other important transport systems.  As proton concentration builds up in the intermembrane space a gradient is created and protons are transported from high to low concentration. The energy from the transfer of protons is used to change ADP into ATP though phosphorolation.  ATP synthase is the protein responsible for ADP phosphorolation. 

It is also important for proper concentrations of substrates to be maintained within and without the mitochondria to allow for chemiosmotic phosphorolation. The two main types of proteins responsible for maintaining proper substrate concentrations are pyruvate and phosphate symporters and ADP/ATP antiporters. 

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Naming Coordination Compounds

A complex is a substance in which a metal atom or ion is associated with a group of neutral molecules or anions called ligands. Coordination compounds are neutral substances (i.e. uncharged) in which at least one ion is present as a complex. You will learn more about coordination compounds in the lab lectures of experiment 4 in this course.

The coordination compounds are named in the following way. (At the end of this tutorial we have some examples to show you how coordination compounds are named.)

A. To name a coordination compound, no matter whether the complex ion is the cation or the anion, always name the cation before the anion. (This is just like naming an ionic compound.)

B. In naming the complex ion:

1. Name the ligands first, in alphabetical order, then the metal atom or ion. Note: The metal atom or ion is written before the ligands in the chemical formula.
2. The names of some common ligands are listed in Table 1.
� For anionic ligands end in "-o"; for anions that end in "-ide"(e.g. chloride), "-ate" (e.g. sulfate, nitrate), and "-ite" (e.g. nirite), change the endings as follows: -ide  -o; -ate  -ato; -ite  -ito
� For neutral ligands, the common name of the molecule is used e.g. H₂NCH₂CH₂NH₂ (ethylenediamine). Important exceptions: water is called ‘aqua’, ammonia is called ‘ammine’, carbon monoxide is called ‘carbonyl’, and the N₂ and O₂ are called ‘dinitrogen’ and ‘dioxygen’.

Table 1. Names of Some Common Ligands

Anionic Ligands	Names		Neutral Ligands	Names
Br-	bromo		NH3	ammine
F-	fluoro		H2O	aqua
O2-	oxo		NO	Nitrosyl
OH-	Hydroxo		CO	Carbonyl
CN-	cyano		O2	dioxygen
C2O42-	oxalato		N2	dinitrogen
CO32-	carbonato		C5H5N	pyridine
CH3COO-	acetato		H2NCH2CH2NH2	ethylenediamine

3. Greek prefixes are used to designate the number of each type of ligand in the complex ion, e.g. di-, tri- and tetra-. If the ligand already contains a Greek prefix (e.g. ethylenediamine) or if it is polydentate ligands (ie. can attach at more than one binding site) the prefixes bis-, tris-, tetrakis-, pentakis-, are used instead. (See examples 3 and 4.) The numerical prefixes are listed in Table 2.

Table 2. Numerical Prefixes

Number	Prefix	Number	Prefix	Number	Prefix
1	mono	5	penta (pentakis)	9	nona (ennea)
2	di (bis)	6	hexa (hexakis)	10	deca
3	tri (tris)	7	hepta	11	undeca
4	tetra (tetrakis)	8	octa	12	dodeca

 

4. After naming the ligands, name the central metal. If the complex ion is a cation, the metal is named same as the element. For example, Co in a complex cation is call cobalt and Pt is called platinum. (See examples 1-4). If the complex ion is an anion, the name of the metal ends with the suffix –ate. (See examples 5 and 6.). For example, Co in a complex anion is called cobaltate and Pt is called platinate. For some metals, the Latin names are used in the complex anions e.g. Fe is called ferrate (not ironate).

Table 3: Name of Metals in Anionic Complexes

Name of Metal	Name in an Anionic Complex
Iron	Ferrate
Copper	Cuprate
Lead	Plumbate
Silver	Argenate
Gold	Aurate
Tin	Stannate

 

5. Following the name of the metal, the oxidation state of the metal in the complex is given as a Roman numeral in parentheses.

C. To name a neutral complex molecule, follow the rules of naming a complex cation. Remember: Name the (possibly complex) cation BEFORE the (possibly complex) anion.See examples 7 and 8.
For historic reasons, some coordination compounds are called by their common names. For example, Fe(CN)₆^3- and Fe(CN)₆^4- are named ferricyanide and ferrocyanide respectively, and Fe(CO)₅ is called iron carbonyl.

Examples Give the systematic names for the following coordination compounds:

1. [Cr(NH₃)₃(H₂O)₃]Cl₃

Answer: triamminetriaquachromium(III) chloride
Solution: The complex ion is inside the parentheses, which is a cation.
The ammine ligands are named before the aqua ligands according to alphabetical order.
Since there are three chlorides binding with the complex ion, the charge on the complex ion must be +3 ( since the compound is electrically neutral).
From the charge on the complex ion and the charge on the ligands, we can calculate the oxidation number of the metal. In this example, all the ligands are neutral molecules. Therefore, the oxidation number of chromium must be same as the charge of the complex ion, +3.

2. [Pt(NH₃)₅Cl]Br₃

Answer: pentaamminechloroplatinum(IV) bromide
Solution: The complex ion is a cation, the counter anion is the 3 bromides.
The charge of the complex ion must be +3 since it bonds with 3 bromides.
The NH₃ are neutral molecules while the chloride carries - 1 charge. Therefore, the oxidation number of platinum must be +4.

3. [Pt(H₂NCH₂CH₂NH₂)₂Cl₂]Cl₂

Answer: dichlorobis(ethylenediamine)platinum(IV) chloride
Solution: ethylenediamine is a bidentate ligand, the bis- prefix is used instead of di-

4. [Co(H₂NCH₂CH₂NH₂)₃]₂(SO₄)₃

Answer: tris(ethylenediamine)cobalt(III) sulfate
Solution: The sulfate is the counter anion in this molecule. Since it takes 3 sulfates to bond with two complex cations, the charge on each complex cation must be +3.
Since ethylenediamine is a neutral molecule, the oxidation number of cobalt in the complex ion must be +3.
Again, remember that you never have to indicate the number of cations and anions in the name of an ionic compound.

5. K₄[Fe(CN)₆]

Answer: potassium hexacyanoferrate(II)
Solution: potassium is the cation and the complex ion is the anion.
Since there are 4 K⁺ binding with a complex ion, the charge on the complex ion must be - 4.
Since each ligand carries –1 charge, the oxidation number of Fe must be +2.
The common name of this compound is potassium ferrocyanide.

6. Na₂[NiCl₄]

Answer: sodium tetrachloronickelate(II)
Solution: The complex ion is the anion so we have to add the suffix –ate in the name of the metal.

7. Pt(NH₃)₂Cl₄

Answer: diamminetetrachloroplatinum(IV)
Solution: This is a neutral molecule because the charge on Pt⁺⁴ equals the negative charges on the four chloro ligands.
If the compound is [Pt(NH₃)₂Cl₂]Cl₂, eventhough the number of ions and atoms in the molecule are identical to the example, it should be named: diamminedichloroplatinum(II) chloride, a big difference.

8. Fe(CO)₅

Answer: pentacarbonyliron(0)
Solution: Since it is a neutral complex, it is named in the same way as a complex cation. The common name of this compound, iron carbonyl, is used more often.

9. (NH₄)₂[Ni(C₂O₄)₂(H₂O)₂]

Answer: ammonium diaquabis(oxalato)nickelate(II)
Solution: The oxalate ion is a bidentate ligand.

10. [Ag(NH₃)₂][Ag(CN)₂]

Answer: diamminesilver(I) dicyanoargentate(I)
You can have a compound where both the cation and the anion are complex ions. Notice how the name of the metal differs even though they are the same metal ions.

Can you give the molecular formulas of the following coordination compounds?

1. hexaammineiron(III) nitrate
2. ammonium tetrachlorocuprate(II)
3. sodium monochloropentacyanoferrate(III)
4. potassium hexafluorocobaltate(III)

Can you give the name of the following coordination compounds?

5. [CoBr(NH₃)₅]SO₄
6. [Fe(NH₃)₆][Cr(CN)₆]
7. [Co(SO₄)(NH₃)₅]⁺
8. [Fe(OH)(H₂O)₅]²⁺

Answers:

1. [Fe(NH₃)₆](NO₃)₃
2. (NH₄)₂[CuCl₄]
3. Na₃[FeCl₁(CN)₅]
4. K₃[CoF₆]
5. pentaamminebromocobalt(III) sulfate
6. hexaammineiron(III) hexacyanochromate (III)
7. pentaamminesulfatocobalt(III) ion
8. pentaaquahydroxoiron(III) ion

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