Monthly Archives: October 2011

3.3 and 7.1 The Structure of DNA

Nucleotides and Nucleic acid

DNA or deoxyribonucleic acid is the genetic material of living organisms making it very important. It is made of simple subunits known as nucleotides. Each nucleotide consists of three parts- a sugar known as deoxyribose, a phosphate group, and a nitrogenous base. DNA nucleotides do not all have the same base. There are four different bases, adenine (A), cytosine (C), guanine (G), and thymine (T). Adenine and guanine are purines whereas cytosine and thymine are pyrimidines. In RNA, uracil is a pyrimidine.

A polymer of nucleotides is known as a nucleic acid. The carbons of sugar molecules have assigned numbers that are used to show points of attachment.

DNA structure

DNA molecules can be linked together by a covalent bond between the sugar of a nucleotide and the phosphate group of another molecule. DNA molecules consist of two strands of nucleotides wound together to form the double helix. Hydrogen bonds link the two strands together and are formed between the bases of two strands. Only adenine and thymine form hydrogen bonds and cytosine and guanine form hydrogen bonds. This is known as complementary base pairing. The two DNA strands are complementary, so the sequence on one strand determines the sequence on the other strand. This complementary feature allows DNA able to self-replicate and also allows DNA to serve as a guide for RNA production.

One strand of the DNA is in the direction of 5 prime to 3 prime while the other is in the direction of 3 prime to 5 prime. The two strands are coiled together which is known as the double helix. A pyrimidine is always facing a purine. While G and C have three hydrogen bonds, A and T only have two bonds.

DNA replication

DNA replication is a way of copying DNA to produce new molecules with the same base sequence. It is semi-conservative meaning that each molecule formed by replication consist of a old and new DNA molecule.

Central dogma of genetics

Reproduction for cells requires transmission of information from parent to offspring. This is termed heredity. A gene is unit of heredity that is coded for by a sequence of DNA bases. Most genes specify the sequence of amino acids in a particular polypeptide. Polypeptides compose proteins and these proteins often directly or indirectly determine characteristics. In transcription, the DNA sequence in a gene is used to create an RNA molecule. These RNA molecules are then decoded into the amino acid sequence of a polypeptide through the process translation.

Nucleosome

In bacteria, DNA is naked but in eukaryotes, DNA is associated with proteins. The most common proteins are histones and they serve to help supercoil DNA to package chromatin and help regulate the expression of genes.

Non-coding sequences

The Human Genome Project has allowed us to understand the many patterns observed in DNA. There are about 25,000 protein-coding genes in the human genome. Some sequences are transcribed to produce other forms of RNA besides mRNA. Because of the diversity of phenotypes it was believed that there were many more genes. It has been found that non-gene factors influence phenotype and on gene expression so this can be one source of diversity. Most of the genome is not transcribed. Originally called ‘junk DNA’, it has been recognized that elements of this ‘junk’ play roles in gene expression and affect repetitive sequences. The repeating sequence are normally between 5 and 300 base pairs long. A repeated sequence can be duplicated as most 105 times per genome.

Introns and exons

Introns are sequences of bases that are transcribed but not translated. Exons are bases of nucleotides hat are both transcribed and translated. Typically, genes of eukaryotes have exons and introns. After transcription, the introns are removed to form mature mRNA in a process known as post-transcriptional modification. Prokaryotes do not have introns.

Data-based question: Chargaff’s data

1. For adenine to guanine and thymine to cytosine humans have a larger amount of the source than wheat. However, for adenine to thymine the amount of the source is the same for humans and wheat (1.0). For guanine to cytosine the numbers are quite close (humans have 1.00 and wheat has 0.97) Also, for purines to pyrimidines the numbers are quite similar (humans have 1.0 and wheat has 0.99)

2a. This is not true because ox and human are the only ones that have 1:1 for guanine to cytosine. The other species have either larger or smaller values.

2b. This ratio is found in many species such as human, yeast, hemophilus influenza, e coli K2, and bacillus schatz. For the other species it is somewhere between 0.99 to 1.02 which is quite close to 1.0

2c. For adenine to thymine, only one speices (human) has this exact ratio. Other species have it somewhere between 0.95 and 1.12.

7.6 Enzymes

Activation and energy

Substrates have to pass through a transition state to get converted into products. Some energy is used to reach transition state but most of the energy is used to go from the transition stage to the product. The energy used to reach the transition stage is known as the activation energy. It is used to break and weaken bonds in the substrates. When enzymes catalyze a reaction, the substrate binds to the active site and then is changed to reach the transition stage. When substrates bind, the overall energy level of the transition state is reduced which reduced the activation energy of the reaction as well. After the transition state, it is then is covered into products that separate from the active sites. The net amount of energy released in not changed by the enzyme but the activation energy is lowered so the rate of the reaction is increased.

The induced-fit model    

Sometimes, the structure and shape of active sites are complementary to the substrates but do not fit. However, binding still occurs. This is known as the induced-fit model, which explains that when substrates bind, they cause the structure of the active site to change to fit the substrates. The structure of the substrates to changed during the transition state. So, during binding, both the substrates and the active sites are altered and this helps weaken or break bonds in the substrate and lower the activation energy.

Enzyme inhibition

Inhibitors are chemical substances that bind to enzymes and reduce enzyme activity. There are two main types of inhibitors, competitive and non-competitive inhibitors.

Competitive Non-competitive
Enzyme Dihydropteroate sythetase Phosphofructokinase
Inhibitor Sulfadiazine Xylitol-5-phosphate
Substrate Para-aminobenzoate Fructose-6-phosphate
Binding The inhibitor binds to the active site reversibly so while it is bound, the substrates can’t bind. The inhibitor binds to a site reversibly away from the active site. While the inhibitor is bound, the active site is distorted so the substrate can’t bind to it.

Metabolic pathways

The word metabolism refers to the many chemical reactions that occur in cells, catalyzed by more than 5000 types of enzymes. There are a few common patterns of metabolism even though it is very complex. Firstly, most chemical reactions occur in a sequence of small steps not one big step and form the metabolic pathway. Secondly, the metabolic pathway includes a chain of reactions. Lastly, some metabolic pathways form a cycle instead of a chain such as the Krebs cycle or the Calvin cycle.

End-product inhibition of metabolic pathways

Allosteric interactions are when the chemical substances bind to special sites on the enzyme that are away from the active site. These special sites are known as allosteric sites. Many times, the enzyme that is regulated catalyzes one of the first reactions in a metabolic pathway. The substance that binds to the allosteric site is the end product, which acts as the inhibitor, of that pathway. The pathway works quickly in cells and can be turned off when there is excess.

This is an economical way to control metabolic pathways because of the concentration of products and its influence on the rate of the reaction. Reactions do not go until completion but instead at an equilibrium position with a ratio of substrates and products. If the concentration of products increases, the reaction will eventually slow down. This effect is echoed back to the metabolic pathway when the end product accumulates and all the intermediates accumulating as well. The end product inhibition prevents this build-up of intermediate products.

Chapter 7 questions

China and India Making Inroads in Biotech Drugs

In class, we recently looked at the article China and India Making Inroads in Biotech Drugs. Cancer drugs and medicines are very expensive and not available in every country at an affordable price. China and India, two of the worlds LEDC’s are copying US’s cancer drugs at a cheaper price without patent. This is angering the US because while they spend millions researching and creating the product, China and India are just copying their hard work and not giving them any profit from that.

There were three basic economic questions in this article. Firstly, what drugs are considered beneficial for all, thus, patents could be violated? Secondly, how could US Biotech companies keep cost competitive with India/ China? Lastly, who will benefit from cheaper drugs? Who will lose?

Some definitions that came up in this article were price discrimination, law of demand, allocation, tradeoff, and opportunity cost. Price discrimination is when the price of a good differs. This is shown as the drugs are sold at a much higher price in the US than in China and India. The law of demand states that as price goes up, quantity demanded goes down and vice versa. This is shown in this article because as the price of the medication in India and China go down compared to the US, the demand for those drugs increase. Allocation is the process of distributing something, in this case money. In this article, the poor people need to decide how to allocate their money so that they can afford the drugs. Allocation shows tradeoffs and opportunity costs because if they do choose to spend their money on the drugs, they are giving up something else that could have been bought with the money spent on drugs.

The stakeholders in this article are the rich and poor patients, pharmaceutical companies, researchers, governments, NGOs, and the Indian and Chinese manufacturers. Though there is no solution that benefits both sides together, there is a possible solution benefiting a few of the stakeholders. The solution is that we can wait 20 years after the product is produced. Once the 20 years are up, the poor people will be able to gain access to these drugs as the second buyers. The first buyers will be the people that are able to afford those drugs in the 20 years. The reason for this solution is that since the pharmaceutical companies are producing the goods and the researchers are finding ways for this to happen, we should side with them since they are the ones putting hard work into the drugs. However, if India and China do not wait for this and keep producing cheaper drugs, US companies will refuse to make newer advances and this will mean that after 20 years, only this cure will remain and no newer improvements or treatments will be produced. In this situation the winners are the rich patients since they will be able to afford the medications as soon as they are out, pharmaceutical companies and researchers because they will be able to gain a profit, and the rich governments (US) because their country will be able to afford medications. The losers will be the poor patients because if anything happens in those 20 years, they will not have treatment as they can’t afford it, the NGOs because they are non governmental, and the Indian and Chinese governments and manufacturers because they will not have treatments for 20 years. In this case, the winners will benefit as they get cures and can possibly make profits while the losers will have costs since many people will be dying in the 20 years they cant afford the drugs. Even if India and China copy the US drugs, they will still have costs because no further advances will be made to the drugs. Looking at this, we can see that the winners such as the US government, pharmaceutical companies, researchers, and rich patients have comparative advantage.

3.6 Enzymes

One gene-one polypeptide hypothesis

Each polypeptide is made by different genes. There is almost always a single gene to code for a polypeptide and does not node any other polypeptide. This founding led to the one gene-one polypeptide hypothesis which is an important hypothesis in molecular biology. There are some exceptions to this rule though. Firstly, some genes code for transfer or messenger RNA and not for polypeptides. Secondly, some DNA sequences act as regulators for gene expression and are not translated to polypeptides. Lastly, in lymphocytes, pieces of DNA from different parts are taken and spliced together to produce antibodies. Different lymphocytes produce different antibodies from the DNA inherited from parents.

Enzymes

Enzymes are globular proteins that are found everywhere and work as catalysts. They speed up chemical reactions without changing themselves by lowering the activation energy. They are often called biological catalysts because they are made by living cells and speed up biochemical reactions. Many enzymes are produced because enzymes only catalyze one biochemical reaction and since many different reactions occur, many different enzymes are needed. The substances that are converted into products in the reactions are called substrates. A typical enzyme only works on the substances used in one reaction and this is called enzyme substrate specificity.

The active site is where substrates bind to special regions on the surface of the enzyme. The shape and properties of the active site and that of the enzyme are complementary so it is able to bind but not other substances. This is the lock and key model and it explains the substrate specificity of enzymes. Substrates are converted into products while they are bound to the active sites then the products get released however the enzymes remain and the active sites can be used over and over again. There are two ways that products are created, through hydrolysis and condensation synthesis. In hydrolysis, the enzyme puts stress on the molecules which makes it split. In condensation synthesis, the enzyme attracts both molecules in the right proximity and orientation and creates one product.

 Effect of pH on enzyme activity

The pH scale is a way to measure the acidity of alkalinity of a solution. The lower the number, the more acid or the less alkalinity that solution has. Also, the lower the pH the more hydrogen ion concentration there is because acidity occurs due to hydrogen ions. The pH scale is logarithmic so each time the pH is reduced one time, it means that the solution is actually ten times more acidic than the previous one. Enzymes are sensitive to pH and have an optimum pH at which their activity is the highest. This optimum depends on the environment the enzymes work in. If the pH is changed from the optimum it will cause the enzyme activity to decrease and eventually stop. When the hydrogen ion concentration is not at the level the enzyme normally works at, it can cause changed in the structure, including the active site of the enzyme. This is known as denaturation.

Effect of temperature on enzyme activity

The temperature can affect enzymes in two ways it can cause enzyme activity to increase and decrease. In liquids, particles are constantly moving randomly so when a liquid is heated, there is more kinetic energy. This causes enzymes and substrate molecules to move due to the increased temperature. When this happens, it can cause the substrate molecules to collide with the active site of an enzyme more often so enzyme activity will increase. Also when enzymes are heated, the bonds in enzyme vibrate more and therefore can break easier. When this occurs, denaturation will occurs meaning that the structure and active site of an enzyme is changed and the enzyme can not catalyze reactions anymore. As more and more enzymes get denatured, the activity falls and will eventually stop.

Enzymes and substrate concentrations

Once substrates bind to the active site, only then can enzymes catalyze reactions. Substrates bind to the active site due to the random movement of molecules in liquid, which result in active sites and substrates to collide. If the concentration of substrates is increased in a solution in a solution with a fixed enzyme concentration, substrates will collide with active sites more frequently and this will cause the rate at which enzymes catalyze reactions to increase. However, after binding to an active site, the active site is occupied and can’t be used for other substrates until the products have been formed and released. So as the concentration of the substrate rises, more and more active sites will be occupied so the rate at which enzymes catalyze reactions will get smaller and smaller as the substrate concentration increases even more.

Using lactase to produce lactose- reduced milk

Lactose is the sugar that is naturally present in milk and can be converted into glucose and galactose by the enzyme lactase. Lactase is acquired from yeast that is cultured by biotechnology companies. Then the lactase is extracted from the yeast and purified for sale to food manufacturing companies.
Lactase is used in food processing for several reasons. Firstly, some people are lactose-intolerant and cannot drink more than 250 mL of milk each day until it is lactose reduced. Secondly, galactose and glucose are sweeter than lactose so less sugar can be added to sweet foods that contain milk. Thirdly, lactose needs to be crystallized during ice cream production so it has a gritty texture. However, glucose and galactose are more soluble so they remain dissolved and give a smoother texture. Lastly, the production is faster for cottage cheese and yogurt because bacteria ferment glucose and galactose faster.

There are two ways that lactase is used during food processing. First, it can be added to milk and the final product contains the enzyme. Second, it can be immobilized on the surface and the milk is then allowed to flow past the immobilized lactase so the product with lactase can avoid contamination.

Data analysis questions: biosynthesis of glycoge

1. There are two different enzymes because there are two bonds in this. There is a 1 to 4 bond and a 1 to 6 bond so there needs to be separate enzymes that catalyze the different formations.

2. The formation of side branches increases the rate at which glucose phosphate molecules can be linked because since there are more chains, more reactions can occur.

3. The shape of Curve A is a positive linear line because of the temperature. Temperature affects the enzyme activity and could denature the enzymes. For this reason, the enzyme is not able to have any more activity because it is denatured.

4a. The shape of Curve B is a line that increases until 35 minutes then starts to become slower.

4b. This happens because, at the beginning, there are many glycogen and substrate molecules that are binding to the active sites. Since more and more active sites are becoming occupied, there are no active sites left so the enzyme activity starts to slow down.

7.5 Proteins

Protein Structure

A chain of amino acids is a polypeptide. There are 20 common occurring amino acids so there is are plenty of proteins because many combinations of amino acids can be made. A primary structure is the sequence of amino acids in a polypeptide. Since the chain of amino acids have polar covalent bonds within the backbones, the polypeptides fold in a way that hydrogen bonds are formed between carboxyl (C=0) group of one residue and the amino acid group (N-H) in another area. This causes the formation of patterns in the polypeptide known as secondary structures. The overall 3-dimensional shape of a protein is known as the tertiary structure. The interactions of the R-group with each other and the water surrounding it cause this shape. There are many types of interactions, one example being the interaction between positively charged R-groups and negatively charged R-groups.

A single polypeptide chain forms some proteins while others are formed from more than one chain. Lysozymes are composed of a single chain so they are polypeptides and proteins. Insulin is formed from two polypeptides. The way that the polypeptides fit together when there is more than just one polypeptide chain is called the quaternary structure. Hemoglobin is made up of four polypeptide chains so the structure is called a quaternary structure. There are two alpha chains, and two beta chains. Each subunit consists of a molecule called a heme group.

The activity of a molecule is related to its structure. Some treatments use high temperatures that can cause changed in the pH and in the structure of a molecule, so the activity is disturbed. When a protein has lost its structure permanently, the protein is denatured.

Molecular visualization software sometimes has a function where the different secondary structures can be seen.

Fibrous and Globular proteins

Protein shapes can be categorized in two categories, fibrous and globular. Fibrous proteins have a long shape, are not soluble in water, and are physically strong. Examples include collagen in skin, keratin in hair, and fingernails. Globular proteins are compact and round and are soluble in water. Examples for this type of protein include enzymes and antibodies.

There are many types of proteins and many different functions. Some of these include sucrase, elastin, insulin, immunoglobulin, Na+/ K+ pumps, and collagen. Sucrases are enzymes that break down sucrose into glucose and fructose and its shape is globular. Elastin is a fibrous protein and is a part of the connective tissue that helps skin recover its shape. Insulin is a hormone involved in regulated blood sugar and its shape is globular. Immunoglobulin helps fight diseases and are also globular. Na+/ K+ pumps are a transport protein in membrane of nerve cells and are globular. Lastly, collagen is a protein strengthening tissue and is fibrous.

Amino acids can be divided into two groups according to the chemical properties of the R group. Polar amino acids have hydrophilic R groups whereas non-polar amino acids have hydrophobic R groups.  The location of the protein and the function it carries out depends on the distribution of these polar and non polar amino acids.

Data-based Question: function of the protein metallothionein

1. Firstly, low concentrations of HgCl2 do not have a very big effect on the BUN in wild-type mice. However, as the concentration increases to 30 and 40 HgCl2/μmol kg-1, the BUN increases as well and has an effect.

2a.  The metallothionein probably helps the mice bare more BUN in their bodies. This is because each time the concentration in both type of mice is measured, the wild-type control mice, or the mice with the metallothionein, has less BUN than the other mice. This means that they have a better chance of living with higher BUN. For example at 0, 20, 30, and 40 HgCl2/μmol kg1, wild-type control mice have less BUN than metallothionein-null mice. Also, at a concentration of 40 HgCl2/μmol kg-1, the wild-type control mice still lived while the metallothionein-null mice did not.

2b.

3. This experiment can be both ethical and non ethical. This is not an ethical experiment because no matter what organism is used, it is still an living organism and should not be used for experiments when it can live a life on its own. On the other hand, this is ethical because

Chapter 4 Questions

1a.Polypeptides are a chain of amino acids. A protein can be a polypeptide if it is made of only one polypeptide, but normally proteins are made up of more than one polypeptide.

1b. Fats are solid at room temperature whereas oil is liquid at room temperature, but both are triglycerides.

1c. Starch is carbohydrates stored in plants whereas glycogen is carbohydrates stored in animals and fungus.

1d. In condensation, water is formed whereas in hydrolysis, water is used to break down the reaction.

1e. Hydrophobic repels water while hydrophilic attracts water.

2a. glucose+ glucose+ water –> maltose

2b. 3 fatty acids + glycerol –> triglyceride +3H2O

2c.

3. The transparency of water is needed for photosynthesis for plants. This is important because plants are very important in the food chain so, the transparency of water is important for all organisms.

4a. Alpha-globin and gamma-globin are present early in gestation.

4b. Gamma-globins are found early in gestation whereas beta-globin is found after 30 weeks of gestation.When gamma-globin declines, beta-globin increases. At 6 months of age, gamma globins are not found anymore whereas beta globins are (about 46% of hemoglobin).

4c. At 10 weeks of gestation, alpha-globin and gamma-globin are found. At 6 months of age, alpha-globin is still found but beta-globin is found as well.

4d. The fetus gets oxygen from the mother’s blood

4e.

5ai. Wild: 13.3 kg

5aii. Captive: 16.2 kg

5b. The lipid content decreases for both the captive and wild birds but more for the captive birds. For the free birds, the lipid content starts off at 11.8 and decreases to 2.2, so the lipid content decreases by 9.6 kg. For the captive birds, the lipid content starts off higher at 12.0 and decreases to 0.8, so the lipid content decreases by 11.2 kg.

5c. It can also be used as a source for insulation.