Monthly Archives: November 2011

8.1 Aerobic respiration: link reaction & Krebs cycle

Anaerobic and Aerobic Respiration

Glycolysis can occur without oxygen so this forms the basis of anaerobic cell respiration. If more oxygen is available, with the release of more energy, pyruvate produced in glycolysis can be oxidized further. For this, the first step is the link reaction and the enzymes in the mitochondrion then catalyze a cycle of reactions called the Krebs cycle.

Link Reaction and The Krebs Cycle

Two molecules of pyruvate are produced in glycolysis per molecule of glucose. If oxygen is available, the pyruvate is absorbed into the mitochondrion and is then fully oxidized.

2CH3 + CO- COOH + 5O2 –> 6CO2 +4H2O

This process involced many steps. The pyruvate from glycolysis is absorbed by the mitochondrion. Enzyme in the matrix of the mitochondrion remove carbon and dioxide from pyruvate and because hydrogen is removed, it is called oxidation. The hydrogen carrier NAD+. and a related compound called FAD, accept these hydrogens. Carbon and oxygen are removed in the form of carbon dioxide, and this reaction is called decarboxylations. Decarboxylation is the removal of carbon dioxide. The first step is when the pyruvate is decarboxylated and oxidized to form an acetyl group and this is called the link reaction because glycolysis links with the cycle of reactions that follow. This cycle has a few names but is commonly known as Krebs cycle. This link reaction involves one decarboxylation and one oxidation. In total in this cycle, there are two more decarboxylations and four more oxidations. In this reaction ATP is produced and this reaction is substrate-level phosphorylation.

If glucose or oxygen were oxidized by burning in the air, energy is released as heat. Most of the energy released in the oxidation fo the link reaction and Krebs cycle is used to reduce the hydrogen carriers. The energy is kept in chemical form and can be passed to the final part of the aerobic cell respiration, oxidative phosphorylation.

3.7 Anaerobic respiration: glycolysis & fermentation

Every cell carries out cellular respiration so that energy can be converted into a form that can be used within the cell. Cells require energy for three main types of activity. Firstly, synthesizing large molecules such as DNA, RNA, and protein. Secondly, pumping molecules or ions across membranes by active transport. Lastly, moving things around inside the cell such as chromosomes vesicles or in muscle cells that cause muscle contraction. The energy for these processes is supplied by ATP. When ATP is split into ADP and phosphate, energy is released.

ATP  usually can’t be absorbed through the plasma membranes so every cell produces its own supplies. Organic compounds containing energy are broken down by enzymes in a controlled way so that as much energy as possible released can be used to form ATP from ADP and phosphate. Cell respiration is defined as the controlled release of energy from organic compounds to form ATP.

Glycolysis and anaerobic cell respiration

Cell respiration can release energy from many organic compounds but it is normally carbohydrates or lipids. If glucoses are used, most organisms begin cell respiration in the same way. Many reactions take place that convert glucose into pyruvate. This chain of reactions is called glycolysis. In glycolysis no oxygen is used and only a small amount of ATP is produced. If no oxygen is available then this is the only ATP that is produced. These are anaerobic conditions and in these conditions, glycolysis can only continue if pyruvates are converted into other substances. In humans pyruvates are converted into lactate (lactic acid). However in year, pyruvates are converted into ethanol (alcohol) and carbon dioxide. These substances are toxic if too much is produced so it must be removed from the cells or produced in limited quantities.

Aerobic cell respiration

If oxygen is available to the cell, pyruvate produced by glycolysis can be oxidized to release more energy. In eukaryotic cells, this occurs in the mitochondria. Energy released from pyruvate oxidation is used for the production of ATP. The amount of ATP per glucose is much higher than glycolysis (more than 10 times). Oxidation of the pyruvate also involves the production of carbon dioxide and water. In most organisms, carbon dioxide is waste and must be removed but the water is useful. In humans about half a liter is produced per day. In animals in desserts, they dont need to drink water and eat dry food because cell respiration supplies their water needs.

Oxidation and Reduction

Oxidation and reduction are chemical processes that occur together. This is because they transfer electrons from one substance to another. Oxidation involves the loss of electrons while reduction involves the gain of electrons. A useful example for biologiest is in Benedict’s test. This involves the use of copper sulfate solution.

Electron Carriers in Cells

Electron carriers are substances that can accept and give up electrons. They often link oxidation and reduction. The main electron carrier in respiration is NAD. NAD has one positive charge and exists as NAD+. It can accept two electrons in a few ways. Two hydrogen atoms can be removed from the substance getting reduced/ One of the hdyrogen atoms is then split into a proton and electron. The NAD+ then accepts the elcton and the proton (H+) is released. The NAD can accept both the electron and proton of the hydrogen atom. These two equations show the reaction.

NAD+ + 2H+ + 2 electrons –> NADH + N+

NAD+ + 2H–> NADH + N+

This shows that reduction is possible by accepting hydrogen atoms because they have an electron. So oxidation can occur by losing hydrogen atoms.

Oxidation and reduction can also occur through oxygen atoms. There are many examples of this because in early evolution of life oxygen was not present in the atmosphere.

Glycolysis

An important consequence of glycolysis is the production of only a small amount of ATP without the use of oxygen by converting sugar into pyruvate. This is done in many steps.

glucose –> fructose –(ATP->ADP)–> fructose phosphate –(ATP->ADP)–> fructose biphosphate

These reactions reduce the activation energy required for reactions that follow these and so these make them easier. In the next step, fructose bisphosphate is split to form two molecules of triose phosphate. Each of these triose phosphate is oxidized to another molecule in a reaction that creates enough energy to make ATP. This oxidation occurs by removing hydrogen atoms. The hydrogen is then added to NAD+ to form NADH+ H+. In the final stages of glycolysis, the phosphate group is transferred to ADP so that more ATP is produced and pyruvate is produced.

3.5 and 7.4 Protein Synthesis

Genes and Polypeptide

Polypeptides are chains of amino acids. There are twenty possible amino acids available to form parts of polypeptides. To make these polypeptides, amino acids must be linked in a specific sequence determined by the information in genes, stored in a coded form. The information in a gene is decoded during the making of a polypeptide. There are two stages of this process, transcription and translation.

Differences between DNA and RNA

DNA and RNA both consist of chains of nucleotides, and are composed of a sugar, phosphate and base. However there are three differences between them. Firstly, while DNA has two strands that form a double helix, RNA has one strand only. Secondly, the sugar in DNA is called deoxyribose whereas the sugar in RNA is known as ribose. Lastly, DNA has the bases A, C, G, and T, whereas RNA has A, C, and G but instead of a T, has U, or uracil.

Transcription

Instead of the being used directly in polypeptides, a copy of the DNA in genes is made instead. This copy is known as RNA and it carries the information needed to make a polypeptide to the cytoplasm so it is called mRNA or messenger RNA. Transcription is the process of copying the base sequence of a gene by making a RNA molecule. The same rules for complementary base pairs are used with the exception of thymine, which is replaced by uracil since RNA does not contain thymine. So the RNA molecule produced is complementary to the transcribed strand but does not contain T and instead contains U.

In the process of transcription, first the DNA double helix uncoils and the two strands separate. Free RNA nucleotides are accumulated using one of the DNA strands as the template, or the transcribed strand. Next, the RNA nucleotides link to form a RNA strand. Then, the mRNA separates from the DNA, and the DNA double helix reforms. This process is carried out from the 3 prime end to 5 prime end.

Translation

Using mRNA and tRNA, translation is carried our by ribosomes. The genetic code is translated in this process. The genetic code is a triplet code, meaning that three bases are used. This group of three bases is called a codon and they code for one amino acid. In the process of translation, first the mRNA binds to the small subunit of a ribosomes. The mRNA contains codons, each of which codes for one amino acid. Around the ribosomes, many tRNA are present, and each tRNA has an anti-codon and carries the amino acid that corresponds to the anti-codon. The tRNA bind to the ribosomes two at a time, but can only bind if the anticodon is complementary to the codons on the mRNA and follow the same base pairing rules. If these bases are complementary, hydrogen bonds are created. Next, the two amino acids carried by the tRNA are linked by a peptide linkage and so a dipeptide is formed, attached to the tRNA on the right. The ribosome moves along the mRNA to the next codon and another tRNA binds. Now three amino acids are linked, and this process occurs until a polypeptide is formed.

3.5 and 7.4 DNA to Protein

Translation
The base sequence of the mRNA molecule is used as a template for the sequence of amino acids that will form a polypeptide. This process is known as translation. The genetic code converts the base sequence on mRNA to an amino acid sequence. This can be applied to languages. The genetic code represents the dictionary that converts Japanese (mRNA) to English (amino acids). A sequence of three nucleotide bases on the mRNA is a codon. Each codon codes for a specific amino acid that is added to the polypeptide. Each amino acid is carried by a specific tRNA, which has a three-base anti-codon that is complementary to the codon on mRNA. If they are complementary, they can attach. In terms of a table, the first position is 5’ end, next is the second position, and the third position is the 3’ end. There is one stop codon and three stop codons. Because some codons can code for the same amino acid, the code is ‘degenrate’. The genetic code is universal and operates in the same way for all like forms on Earth. However there are some expcetions such as some stop codons being used to code non-standard amino acids.

After mRNA is transcribed, it leaves the nucleus and enters the cytoplasm and translation occurs. Translation takes place on ribosomes. Each ribosome has a small and large subunit. First, mRNA binds to the small subunit of a ribosome. tRNA molecules are present and each one carries the specific amino acid that corresponds to the anti-codon. The tRNA binds to the ribosomes at the site where the anti-codon and codon math. Two tRNAs binds at the same time and the first one transfers the growing polypeptide chain to the next one. The ribosome moves along the mRNA and this process continues until they reach a stop codon and the polypeptide is released. Basically, tRNA enters, binds to the ribosomes, moves, then exits.

Details of translation

Each tRNA molecule is recognized by a tRNA-activating enzyme that binds a specific amino acid to the tRNA, using ATP. There are 20 tRNA-activating enzymes, one for each amino acid. The amino acids attaches at the 3’ end of the tRNA, and this terminates with the sequence CCA.

Ribosomes are made of ribosomal RNA, or rRNA and many large individual proteins. Each ribosome is made up two subunits, one large one and a small one. IT has three tRNA binding sites, the ‘E’ site which is the exit site, the ‘P’ or peptidyl site, and the ‘A’ or aminoacyl site. Someitmes, more than one ribsome can translate the same mRNA molecule at the same time. The resulting complex of ribosomes on a single mRNA is called a polyribosome or polysome. Translation always starts in the cytoplasm. IF the proteis are destined vetually for lysosome or export then the ribosomes bind to the endoplasmic reticulum for translation to be completed.

The Stages of Translation

  • An mRNA molecule binds to the small ribosomal subunit at the binding site. An initital tRNA molecules binds at the start codon.
  • The large ribosomal subunit arrives
  • The next codon signals another tRNA to bind.
  • A peptide bodn is formed between the two amino acids, one in the ‘A’ site and the other amino acid in the ‘P’ site.
  • The ribsome moves the first tRNA into the ‘E’ site so that the next codon can attach to the ‘A’ site and add to the growing amino acid chain on the tRNA in the ‘P’ site.
  • The process continues until a stop codon is reached when the polypeptide is rfree. The direction of the movement of mRNA is from the 5’ end to the 3’ end of mRNA.

Exam questions on Topic 7:

1ai. The temperature for x was higher than 40 degrees Celcius. This is because at the beginning, the substrate rate was faster however over time the concentration remained constant due to denaturation of the enzyme.

1aii. The temperature could be around 30 degrees because the rate is very slow but it is not remaining constant showing that the enzyme has not denatured but the rate is just very slow.

1bi/ 1bii.

2a. The 3’ terminal is the sugar (deoxyribose for DNA and ribose for RNA) where nucleotides are linked. The 5’ terminal is the phosphate group where nucleotides are linked.

2b. Firstly, purines are double ringed whereas pyrimidines are singled ringed. Also, purines contain adenine while pyrimidines contain cytosine, thymine (only for DNA), and uracil (only for RNA).

2c. Firstly in transcription, DNA is transcribed whereas in translation, mRNA is translated. Secondly, RNA polymerase does transcription whereas translation is done by ribosomes. Lastly, RNA is produced in transcription whereas amino acids are joined to form polypeptides in translation.

3a. This is a globular protein.

3b. The primary structure of the protein is the sequence and number of its amino acids.

3ci. X= beta pleating, Y= alpha helix

3cii. To stabilize these structures, hydrogen bonds are used.

3d. The tertiary structure is very important because it enables the protein to have its shape such as the beta pleating and also determines the shape of the enzymes active site.

3.5 and 7.3 DNA to RNA

Transcription

In transcription, mRNA is made. tRNA also has a role in transcription as well as rRNA which is a functional component of ribosomes. RNA is single stranded, therefore transcription occurs only on one strand. The sequence of the RNA produced is complementary to the DNA that is used as a template. In transcription, first the enzyme RNA polymerase binds to the promoter, which is a site on the DNA. This is known as the initiation stage. The promoter determines which of the two DNA strands will be transcribed. Next, RNA polymerase unwinds and separates the DNA that is going to be transcribed. RNA nucleotides pair with their complementary bases of one DNA strand. However, RNA does not have thymine so uracil is used instead. Next, RNA polymerase forms covalent bonds between the nucleotides. Nucleoside phosphates are only added at the three prime end so the RNA transcript grows in the 5’ to 3’ endAs it moves along the DNA, it unwind and winds after transcription is completed over the segment. . This is known as the elongation stage. Lastly, RNA separate from the DNA when RNA polymerase reaches a termination site and the double helix now reforms. This is known as the termination stage.

Details of Transcription

The two sections of DNA that are involved in transcription are complementary. One sequence is “sense” while the other sequence is “anti-sense”. The mRNA created in transcription is also “sense” and is complementary to the “anti-sense” strand, which was used as the template.

In eukaryotes, the immediate product of mRNA transcription is pre-mRNA because it must go through many stages of post-transcriptional modification to become mature. One of these stages is RNA splicing, which removes the introns and leaves the exons. Introns are non-expressed genes and they do not contribute to the formation of introns. Once the introns are removed, the remaining coding portions are exons. The exons are expressed genes and are spliced together to form mature mRNA.

Translating the Genetic Code

mRNA contains the information needed for making polypeptides in the cytoplasm of eukaryotes. This information is decoded and translated during translation. The base sequence of mRNA is translated into the amino acid sequence of a polypeptide. The meaning of each codon is shown in the table on the left.

The genetic code is a triplet code with three bases that code for one amino acid. A group of three bases is called a codon. So one codon codes for one amino acid. There are 64 different codons available. This gives more than enough codons to code for the 20 possible amino acids. Because more than two codons can cod for the same amino acid, this code is degenerate. This code is also universal with a few exceptions.

3.4 and 7.2 DNA replication

Semi-conservative replication

When a cell is about to divide, the two strands of the helix separate. Each of the strands acts as guides for creating new strands. This will mean that each DNA molecule will be composed of a new and original strand, making it semi-conservative. The sequence of one DNA strand determines the sequence of the other DNA strand, so they are complementary.

There are a few ways for DNA replication to occur. In DNA replication, a large number of enzymes are involved are involved in the process so for these enzymes to gain access to the DNA, the helix has to be separated and unwound by the enzyme DNA helicase. This is done by breaking down hydrogen bonds. These strands now act as templates for new strands.

Within the process, hydrogen bonds bond the nucleotides with their complementary bases. DNA polymerase links the phosphate of the new DNA nucleotide to the sugar of the nucleotide by a covalent bond.

DNA replication

There are a few differences between DNA replication in prokaryotes and eukaryotes but they are very similar. Replication begins at sites called origins of replication. In prokaryotic cells there is one site whereas in eukaryotic cells there are many. Replication occurs in both directions starting from the origin.

During replication, 5 essential enzymes are used and each new unit that is added to the growing nucleic acid is a nucleoside triphosphate. A nucleoside is a sugar and a nitrogenous base. A nucleoside triphosphate hydrogen bonds to its complementary base in the exposed DNA molecule. The hydrolysis of two molecules of phosphate occurs to convert the nucleoside triphosphate to a nucleotide. This hydrolysis of phosphate also provides energy that is necessary to add the nucleotide to the growing polymer. The enzyme DNA polymerase III extends the DNA by adding nucleotides to the three prime end using condensation and this requires a short sequence known as a primer to start the process. The primer is made of RNA and by the enzyme primase (RNA primase). DNA polymerase I is the enzyme that later takes away the RNA primase and replaces it with DNA.

The nucleoside triphosphates can only be added at the carbon 3 end of the nucleotide before it. Because the DNA strands are organized anti-parallel to each other, the DNA must be synthesized in a continuous fashion or discontinuous fashion. Because nucleotides are always added at the 3 prime end, the strand from 5’ to 3’ is the leading strand. However, since the other side is facing the other direction, replication is discontinuous and occurs by fragments known as Okazaki fragments. These fragments are later joined together by DNA ligase.

Data-based question: evidence for discontinuous DNA synthesis

1. Firstly, the sample that was pulsed for 30 seconds has more molecules closer to the top than the sample pulsed for 10 seconds does. This proves that the molecules sampled for 30 seconds are smaller. Secondly, the sample of 30 seconds has two peaks whereas the sample of 10 seconds only has one peak. This shows the placement of the molecules during the samples.

2. There are two peals for the 30-second sample. The first peak is higher which shows that there are a large number of smaller fragments. These fragments are Okazaki fragments therefore this peak represent the lagging strand. The second peak is lower showing a smaller number of smaller fragments and larger fragments. Because there are larger fragments, this represents the leading strand.

3. DNA ligase combines smaller fragments to form bigger fragments. This is shown through the 60 second sample because in the middle, the number of smaller fragments are very high but start to decrease. Because DNA ligase forms larger fragments, and the number of larger molecules ahs increased while the number of smaller molecules has decreased, this provides evidence for DNA ligase activity.