1. What are the chemical elements that form most of living biological matter?
The chemical elements that form most of the molecules of living beings are oxygen (O), carbon (C), hydrogen (H) and nitrogen (N).
2. Living beings are made of organic and inorganic substances. According to the complexity of their molecules how can each of those substances be classified?
Inorganic substances, like water, mineral salts, molecular oxygen and carbon dioxide, are small molecules made of few atoms. Organic substances, in general, like glucose, fatty acids and proteins, are much more complex molecules made of sequences of carbons bound in carbon chains. The capacity of carbon to form chains is one of the main chemical facts that permitted the emergence of life on the planet.
Biochemistry Introduction Review - Image Diversity: carbon chains
3. What are the most important inorganic molecular substances for living beings?
The most important inorganic substances for living beings are water, mineral salts, carbon dioxide and molecular oxygen. (There are several other inorganic substances without which cells would die.)
4. What are mineral salts? Where in living beings can mineral salts be found?
Mineral salts are simple inorganic substances made of metallic chemical elements, like iron, sodium, potassium, calcium and magnesium, or of non-metallic elements, like chlorine and phosphorus.
They can be found in non-solubilized form, as part of structures of the organism, like the calcium in bones. They can also be found solubilized in water, as ions: for example, the sodium and potassium cations within cells.
5. What are the most important organic molecules for living beings?
There are many types of organic molecules that are important for the living beings. Especially important are amino acids and proteins, carbohydrates (includingglucose), lipids and nucleic acids (DNA and RNA).
Biochemistry Introduction Review - Image Diversity: amino acid molecule protein molecule carbohydrate molecule lipid molecule nucleic acid molecule
6. What are the main functions of the organic molecules for living beings?
Organic molecules, like proteins, lipids and carbohydrates, perform several functions for living organisms. Noteworthy functions are the structural function (as part of the material that constitutes, delimits and maintains organs, membranes, cell organelles, etc.), the energetic function (chemical reactions of the energetic metabolism), the control and informative function (genetic code control, inter and intracellular signaling, endocrine integration) and the enzymatic function of proteins (facilitation of chemical reactions).
7. What are some examples of the structural function of organic molecules?
Organic molecules have a structural function as they are part of cell membranes, cytoskeleton, organ walls and blood vessel walls, bones, cartilages and, in plants, of the conductive and support tissues.
8. What are some examples of the energetic function of organic molecules?
Since they are complex molecules, presenting many chemical bonds, organic molecules store large amount of energy.
Glucose, for example, is the main energy source for the formation of ATP (adenosine triphosphate), a molecule that is necessary in several metabolic reactions. ATP is an organic molecule too and is itself the energy source for many biochemical reactions. Fat, proteins and some types of organic polymers, like starch and glycogen, that are polymers ofglucose, are energy reservoirs for the organism.
9. What are some examples of the control and informative function of organic molecules?
Based on genetic information, organic molecules control the entire work of the cell. The nucleic acids, DNA and RNA, are organic molecules that direct the protein synthesis, and proteins in their turn are the main molecules responsible for the diversity of cellular biological tasks. In membranes and within the cell, some organic molecules act as information receptors and signalers. Proteins and lipids have an important role in the communication between cells and tissues, acting as hormones,substances that transmit information at a distance throughout the organism.
10. What are biopolymers?
Polymers are macromolecules made by the union of several smaller identical molecules, called monomers. Biopolymers are polymers present in the living beings. Cellulose, starch and glycogen, for example, are polymers ofglucose.
Biochemistry Introduction Review - Image Diversity: starch molecule glycogen molecule
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Water Properties and Mineral Salts Review
1. What is the approximate percentage (in mass) of water in the human body? Is this percentage expected to be larger in the adult or in the old individual?
Approximately 65% of the human individual mass is water. The brain, for example, has around 90% of water in mass, the muscles, 85%, and the bones have between 25% and 40% of water.
Younger adult individuals have proportionally more water in mass than older individuals.
2. What are the main biological functions of water?
Water is the fundamental solvent for chemical reactions of living beings; it is the main means of substance transportation in the cell and between cells and tissues and it is responsible for the maintenance of adequate temperature for the functioning of the organism. Water is also the reagent or the product of many biochemical reactions, like photosynthesis, cellular respiration, peptide bond for protein formation, etc.
3. Water has key participation in organic reactions. What are examples of two types of organic reactions in which water is respectively incorporated or liberated in the products of these reactions?
Photosynthesis is a biochemical process in which water is incorporated into organic molecules. In the reaction, the hydrogen atoms from water go to the produced glucose and the oxygen atoms from water form the molecular oxygen liberated: carbon dioxide + water + light = glucose + molecular oxygen. Aerobic respiration is an example of biochemical reaction in which water is produced: glucose + molecular oxygen = carbon dioxide + water.
Water Properties and Mineral Salts: water molecule
4. Is water a polar or a non-polar molecule? What is the consequence of that characteristic for the function of water as solvent?
Water is made of two atoms of hydrogen attached by covalent bond with one central atom of oxygen making an angular spatial structure. The hydrogen atoms “lend” electrons to the oxygen and consequently this atom becomes more negative while the hydrogens become more positive. The spatial geometry of the water molecule makes it a polar molecule, with negative and positive poles.
Water is an excellent solvent for polar substances because the electrical activity (attraction and repulsion) of its poles helps the separation and the mixing of these substances, giving them more movement and thus increasing the number of molecular collisions and the speed ofchemical reactions. On the other hand, water is not good as a solvent for non-polar substances.
Polarity is one of the water properties.
Water Properties and Mineral Salts: water polarity
5. Which kind of polarity do water-soluble and fat-soluble substances respectively have?
Water-soluble substances are polar molecules, i.e., they have electrically charged areas. These molecules get the description “water-soluble” because they are soluble in water, a polar molecule too.
Fat-soluble substances are non-polar molecules, i.e., they are electrically neutral. They get the description “fat-soluble” because they dissolve other non-polar substances.
6. What is the importance of water for enzymatic activity?
Enzymes, biological catalysts, depend on water to reach their substrates and bind to them. There is no enzymatic activity without water. In addition, enzymes depend on adequate pH interval to work and the pH is a consequence of the liberation of hydrogen cations (H+) and hydroxyl anions (OH-) by acids and bases in water solution.
7. Can the heat capacity of water be considered small or large? What is the biological significance of that characteristic?
From Thermology it is known that the quantity of exchanged heat (Q) is equal to the mass (m) multiplied by the specific heat of the substance (c) multiplied by the variation of temperature (T), Q = m.c.ΔT., and that heat capacity is Q/T, hence, m.c. Heat capacity, however, relates to a specific body, since it considers mass, whereas specific heat relates to the general substance. Therefore it is more correct to refer to specific heat in this problem.
Water has a specific heat of 1 cal/g.oC which means that 1 oC per gram is changed in its temperature with the addition or subtraction of 1 cal of energy. This is a very elevated value (for example, the specific heat of ethanol is 0,58 cal/g oC, and mercury, a metal, has a specific heat of 0,033 cal/g. oC) making water an excellent thermal protector against variations of temperature. Even if sudden external temperature changes occur, the internal biological conditions are kept stable in organisms which contain enough water.
High specific heat is one of the most important water properties.
8. What are the main water properties that make water special for life?
The water properties that make water biologically important are molecular polarity, thermal stability (elevated specific heat), fusion and ebullition points that allow water to be liquid in most environments, acid-base neutrality, small molecular size and low chemical reactivity. (Compared to other substances, like ethanol or hydrogen sulfide.)
9. What are ions? What are the two types of molecules into which ions are classified?
Ions are atoms or substances electrically charged by means of loss or gain of electrons.
The two types of ions are the cations and the anions. Cations are ions with positive total electric charge and anions are ions with negative total electric charge.
10. Which are the main positive ions found in living beings?
The main cations found in living beings are the sodium cation (Na+), the potassium cation (K+), the calcium cation (Ca++), the iron cations (Fe++, Fe+++), the magnesium cation (Mg++), the zinc cation (Zn++) and the manganese cation (Mn++).
11. What are the main negative ions found in living beings?
The main anions found in living beings are the chlorine anion (Cl-), the phosphate anion (PO4--), the bicarbonate anion (HCO3-), the nitrate anion (NO3-) and the sulfate anion (SO4-).
12. How do mineral salts participate in osmotic regulation?
Osmotic pressure depends on the number of particles dissolved in a solution and not on the nature of such particles. Mineral salts, glucose, proteins and urea are the main regulating particles for the osmolarity of the organism. These molecules along with other particles inside and outsidethe cell generate the larger or smaller osmotic gradient between the intracellular and the extracellular space.
13. What is the role of mineral salts in the creation of electric tension (voltage) at the cellular level?
The electric activity of the cell, for example, in neurons, depends on the different concentrations of positive and negative ions between the inner and the outer surfaces ofthe cell membrane. Mineral salts are responsible for that voltage.
The cell membrane of non-excited cell has commonly a negative inner side and a positive outer side. This electrical situation is maintained by ion transport across the membrane.
14. Why is pH regulation important for living beings? How do mineral salts participate in this regulation?
The potential of hydrogen (pH) is a measure of the amount of hydrogen ions (H-) in a solution. The regulation of the pH according to the necessities of each organ or tissue is extremely important for the organism since enzymes act only under some pH ranges and many proteins are only active under some pH ranges. Therefore biochemical reactions depend on correct levels of pH to occur.
Neutral pH is one of the water properties.
15. How do mineral salts participate in enzymatic activity?
Many mineral salts are cofactors of enzymes, i.e., they are substances without which enzymes do not work.
16. What are the main biological processes in which calcium participates?
Calcium is present in almost all cells and has several functions.
Calcium has an important role in muscular contraction, in the blood coagulation process, in the structure of bone tissue, in teeth, in the motility of the sperm cell flagellum and in the nervous transmission.
17. What is hemoglobin? What is the inorganic element that is fundamental in the composition of hemoglobin?
Hemoglobin is the protein present in the blood responsible for the transport of oxygen from the lungs to the tissues and cells.
The hemoglobin molecule is composed of four protein chains, each with a heme group containing an iron atom. The iron is responsible for the binding of oxygen in the lungs and also for the red color of hemoglobin and thus of the blood.
Water Properties and Mineral Salts: hemoglobin molecule heme group
18. What is the importance of magnesium for plants? What are the other main biological functions of magnesium?
Magnesium is fundamentally important for plants because it is part of the chlorophyll molecule (and chlorophyll is essential for photosynthesis).
Magnesium also acts as a cofactor of several enzymes and it is important the muscle relaxation and for the nervous transmission.
19. What is phosphorylation? What are some biological processes in which phosphorylation plays a critical role?
Phosphorylation is the name given to processes of the addition of phosphates to some molecules thus making these molecules more energized. Phosphorylation has an important role, for example, in photosynthesis (the photophosphorylation of the light phase) and in aerobic respiration (oxidative phosphorylation of the respiratory chain). In general the phosphate used in phosphorylation comes from ATP molecules.
20. Why is iodine important for human beings?
Iodine is a fundamental chemical element for the proper functioning of the thyroid since it is part of the hormones produced by this gland. Iodine deficiency creates a kind of hypothyroidism, a disease known as endemic goiter.
21. What are the main biological functions in which chlorine ions participate?
Like sodium cations, chlorine anions actively participate in the regulation of the osmolarity of tissues and cells by crossing the cellular membrane and avoiding entrance of water into the cell or excessive loss of water from the cell. Chlorine anions have an important role for the acid-base balance of the organism since they participate, along with bicarbonate anions, in the pH buffer system of the body. Another function of chlorine is in the digestive physiology: inside the gastric lumen, hydrochloric acid secreted by stomach cells ionizes itself into hydrogen and chlorine ions lowering the pH of the gastric juice and then permitting the enzymatic digestion to take place.
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Carbohydrates Properties Review
1. What are the organic chemical groups that characterize carbohydrates? How are carbohydrates classified according to the presence of those groups?
Carbohydrates are also known as sugars (starches, cellulose and other substances are carbohydrates too).
Carbohydrates are polyhydroxylated aldehydes or polyhydroxylated ketones (polyalcohol aldehydes or polyalcohol ketones).
Polyhydroxylated aldehydes are called aldoses and polyhydroxylated ketones are called ketoses.
2. What is the molecular formula of glucose? How can its structural formula be described?
The molecular formula of glucose is C6H12O6.
Structurally glucose is a hexagonal ring formed by one atom of oxygen and five atoms of carbon; a hydroxyl radical and a hydrogen atom bind in each carbon of the ring, except for one of the carbons bound to the oxygen of the ring; this carbon binds to a CH2OH radical. Spatial sides of hydroxyl bonds are alternated.
Carbohydrates Properties Review - Image Diversity: glucose molecule
3. What are monosaccharides, oligosaccharides and polysaccharides?
Monosaccharides are simple molecules of carbohydrates that cannot be broken into smaller molecules of other carbohydrates. Oligosaccharides are carbohydrates made by union of a maximum of 10 monosaccharides. Polysaccharides are polymers of monosaccharides made of more than 10 units of such monomers. The most important polysaccharides are cellulose, starch, glycogen and chitin.
4. What is the difference between monosaccharides and disaccharides? What are some examples of disaccharides and of monosaccharides that form them?
Monosaccharides are simple molecules of carbohydrates that cannot be broken into other carbohydrates. Glucose and fructose are examples of monosaccharides. Disaccharides are carbohydrates made of two monosaccharides and with the loss of one molecule of water (dehydration). The chemical bond between two monosaccharides is known as a glycosidic bond.
Sucrose (table sugar) is a disaccharide made by the union of one molecule of glucose with one molecule of fructose. Maltose is a disaccharide made by two glucose molecules. Lactose (milk sugar) is another disaccharide and it is created by the union of one molecule of galactose with one molecule ofglucose.
5. What are hexoses? What are some examples of hexoses with important biological functions?
Hexoses are carbohydrates made of six carbons. Glucose, fructose and galactose are examples of hexoses. Hexoses have an important biological role as energy sources for the metabolism.
Carbohydrates Properties Review - Image Diversity: fructose molecule sucrose molecule
6. What are pentoses? What are the roles of pentoses in DNA and RNA molecules?
Pentoses are carbohydrates made of five carbons.
The DNA molecule is made of a sequence of molecules called nucleotides. Each nucleotide is formed by the association of one pentose called deoxyribose with a phosphoric acid and a nitrogen-containing base (A, T, C or G). RNA is also formed by a sequence of nucleotides. The RNA nucleotides are made by association of one ribose (a pentose) with one phosphoric acid and one nitrogen-containing base (A, U, C or G).
So pentoses are fundamental components of DNA and RNA.
Carbohydrates Properties Review - Image Diversity: pentoses
7. What are the main biological functions of the polysaccharides?
Polysaccharides have an energy storage function and a structural function. Polysaccharides incorporated by living beings along the food chain are important sources of carbohydrates for the energetic metabolism of organisms of the next trophic levels.
Starch is the polysaccharide used for energy store by plants. Glycogen is a macromolecule responsible for the storage of glucose in the liver and muscles. Chitin is a polysaccharide with structural functions that constitutes the exoskeleton of the arthropods and the cell wall in fungi.
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Fat Review - Lipids Q&A
1. What are the main types of lipids?
The main types of lipids are triglycerides (fats and oils), phospholipids, waxes and steroids.
2. What is the structural formula of glycerol? To which organic function do these molecules belong?
Glycerol is a linear chain of three carbons; the central carbon is bound to one hydroxyl radical and to one hydrogen and the two other carbons in the extremities are bound to a hydroxyl radical and to two hydrogens. Spatial sides of the hydroxyls are the same.
Lipids and Fat Review - Image Diversity: glycerol molecule
3. How are triglycerides made?
Triglycerides, fats or oils, are made of three molecules of fatty acids bound to one molecule of glycerol. Hydroxyls of each one of the three fatty acids and each hydrogen of the hydroxyls of the glycerol bind to form three molecules of water that are liberated.
Lipids and Fat Review - Image Diversity: triglyceride molecule
4. What are phospholipids?
Phospholipids are molecules made of glycerol bound to two long molecules of fatty acids and to one phosphate group. Therefore, phospholipids are amphipathic molecules, i.e., they have a non-polar portion, due to the long fatty acid chains, and a polar portion, due to the group phosphate.
Phospholipids are the main component of cell membranes. Sphingomyelin, the substance that forms the myelin sheath of axons in the nervous system, is a phospholipid too.
Lipids and Fat Review - Image Diversity: phospholipid molecule
5. What are steroids? What are some examples of steroids with a biological function?
Steroids are lipids based in an angular combination of four carbon rings, three of them made of six carbons and one ring made of five carbons in the extremity. The union of each ring to the adjacent ring is made by the sharing of two adjacent carbons belonging to both rings.
Bile salts, cholesterol, the sexual hormones estrogen, progesterone and testosterone, the corticosteroids and the pro-vitamin D are examples of steroids.
Lipids and Fat Review - Image Diversity: steroid structure
6. What are hydrophobic molecules (or hydrophobic molecular regions)? What are hydrophilic molecules? How can they be characterized in relation to their polarity?
Hydrophobic molecules are those that have little or no propensity to dissolve in water (hydro = water, phobia = fear). Hydrophilic molecules are those that have great propensity to dissolve in water (philia = friendship).
Water is a polar substance. Remembering the rule that “equal dissolves equal” one can conclude that hydrophobic substances are non-polar molecules while hydrophilic molecules are polar molecules.
7. Are organic solvents like benzene and ether polar or non-polar substances?
Benzene and the ethers are molecules without electrically charged portions and thus they are non-polar substances.
8. Regarding solubility, how are lipids classified?
Fats and oils are hydrophobic molecules, i.e., they are non polar and insoluble in water. Lipids in general are molecules with a large non-polar extension and so they are soluble in non polar solvents, like benzene, ether and chloroform.
There are some amphipathic lipids, i.e., lipids whose molecules have a hydrophilic portion, like the phospholipids, giving them the property of being dragged by water, and a hydrophobic portion (non polar).
9. What is meant by saturation or unsaturation of oils and fats?
When it is said that a triglyceride is saturated it means that in its molecule the carbon chain is bound in its maximum capacity to hydrogens, i.e., there are no double or triple bonds between carbons. These saturated molecules are generally solid fats at normal temperature.
Unsaturated triglyceride molecules are those in which there are double or triple bonds between carbons and so they do not accomplish their maximum capacity of hydrogenation. These unsaturated molecules in general are oils, liquid at normal temperature.
The terms saturated or unsaturated refer then to the saturation of the carbonic chain by hydrogen atoms.
Lipids and Fat Review - Image Diversity: saturated fatty acid unsaturated fatty acid
10. Why do fats have thermal isolation properties?
Triglycerides are weak heat conductors and in addition they form thick layers of fat tissue when accumulated by the organism. That is why they are good thermal isolators.
In animals that live in cold climates, like polar bears, seals and whales, the adipose tissue helps the maintenance of the internal body temperature.
11. How are lipids used as an energy source by the organism?
Carbohydrates are the main energy source for aerobic cell respiration. In the absence or deficiency of such substances the organism can use lipid stores since fats (like proteins) can be degraded into acetyl-CoA to feed the Krebs cycle (a stage of the aerobic cellular respiration).
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Protein Structure Review
1. What are proteins? How can the protein diversity of living beings be explained?
Proteins are molecules made of sequences of amino acids bound by a peptide bond.
The genetic code codifies twenty different amino acids that can compose proteins. So there are numerous combinations of amino acid which can form polypeptide chains and for this reason protein molecules can be immensely diverse.
2. What is the importance of proteins for living beings?
Proteins play a fundamental role in nearly all biological processes. Due to their diversity they can assume many different configurations and they can play varied roles in cells and tissues.
Some protein functions are noteworthy: the structural function (cell membrane proteins, cytoskeleton proteins, proteins of the connective tissue), the enzymatic function (enzymes are proteins), the energy storage function (proteins can be degraded into acetyl-CoA and “cycle” the Krebs cycle), the osmotic regulation function (albumin), the transportation function (membrane channels, respiratory pigments), the immune protection function (antibodies), the movement function (contractile proteins), the endocrine integration function (hormones) and the informative function (membrane receptors, intracellular signalers). There are also many proteins whose biological functions are not yet known.
3. What is the constitutional unit of proteins?
The constitutional units of proteins are the amino acids.
Protein Structure Review - Image Diversity: amino acid structure
4. What is an oligopeptide? How is it different from a polypeptide?
Peptide is the molecule formed by the union of amino acids through the peptide bond. Oligopeptide is a peptide made of few amino acids (oligo = few). Polypeptides are peptides with many amino acids (poli = many), in general more than 50.
5. How many are the known amino acids that form proteins in living beings?
There are twenty different known amino acids that form proteins related to the genetic code of the living beings.
There are still many other amino acids as yet not known.
Protein Structure Review - Image Diversity: types of amino acids
6. Does every amino acid have a central carbon? To which organic group is that central carbon bound?
A carboxyl group –COOH, an amine group – NH2, an atom of hydrogen –H and a variable radical -R necessarily are bound to the central carbon of an amino acid.
7. How can amine groups be classified?
Amines can be classified into primary amines, those to which one –R (variable radical) is attached to a –NH2, secondary amines, those where one hydrogen of NH2 is substituted by another –R, thus having two –R, and tertiary amines, those with no hydrogen bound to the nitrogen and with three –R.
primary amine secondary amine tertiary amine
8. What is the structural representation of a carboxyl group?
Carboxyl groups have a carbon attached to one hydroxyl group by a simple bond and to one oxygen by a double bond. The other site of binding in the carbon is available to other chemical entities.
9. What is the structural flat representation of an amino acid molecule?
An amino acid has a central carbon to which a carboxyl group binds on a side and to which a –R (variable radical) binds on the opposite side. In the perpendicular direction of those ligands an amine group binds the central carbon on one side and a hydrogen binds on the opposite side.
The bind of the carboxyl group to a carbon where a hydrogen is laterally attached is responsible for the name “acid” in amino acids. The bound of an amine group in the central carbon provides the name “amino”.
Protein Structure Review - Image Diversity: carboxyl group
10. What is the importance of the –R group (variable radical) in an amino acid molecule?
The –R group, also called a lateral chain, is the variable part of the amino acid molecule. The –R group can be a complex carbonic chain, a substituting methyl group (forming then the amino acid alanine) or even only a hydrogen (forming glycine, the simplest amino acid). So the –R group is important because it is the differentiation factor ofamino acids.
11. How can the binding of two amino acids for the peptide formation be described?
A peptide is formed when a carbon from the carboxyl group of one amino acid is connected to the nitrogen of the amine group of another amino acid. During that binding the hydroxyl of the carboxyl and one hydrogen of the amine is lost resulting in the liberation of one water molecule.
12. What is the binding between two amino acids called?
The chemical bond between two amino acids is called a peptide bond.
Protein Structure Review - Image Diversity: peptide bond
13. Do the –R groups bound to the central carbons participate in the union between amino acids?
The peptide bond attaches the nitrogen of the amine group of one amino acid to the carbon of the carboxyl group of another amino acid liberating one molecule of water. So the –R groups do not participate in that bond.
14. Do the –H groups bound to the central carbons participate in the peptide bond?
The central carbons themselves, the –R groups and the hydrogens attached to the central carbons do not participate in the peptide bond.
15. Do the amine and the carboxyl groups attached to central carbons participate in the union between amino acids?
Yes. The nitrogen of the amine group of one amino acid binds to the carbon of the carboxyl group of the other amino acid. The water molecule liberated from the formation of thepeptide bond thus has a hydrogen from the amine and an oxygen and another hydrogen from the carboxyl.
16. Does the chemical reaction to unite amino acids incorporate or liberate atoms? What are the chemical entities incorporated or liberated in this reaction?
The union of amino acids by peptide bond liberates atoms. They are liberated as constituents of one molecule of water.
17. Are there different proteins made by the same total number of amino acids?
Different proteins with the same total number of amino acids may exist. In such cases the differentiation is given by the types of amino acids or by the sequence in which they form the protein.
18. Are proteins with the same number of each different amino acid that form them necessarily identical proteins?
Even if many proteins have the same number of each different amino acid that form them, for example, 50 alanines, 70 glycines and 20 histidines, the sequences in which theseamino acids are connected may be very different. So if two or more proteins are in such condition of numeric similarity for each type of their constituentamino acids, they are not necessarily identical.
19. What is the essential condition for a protein to be identical to another protein?
For a protein to be identical to another protein it is necessary for the sequence of amino acids that form them to be identical.
20. What is the primary structure of a protein? What is the importance of the primary structure?
The primary protein structure is the linear sequence of amino acids that form the molecule.
The primary structure is the basis of the protein identity. Modification of only one amino acid of the primary structure creates a different protein. This different protein can be inactive or can even have other biological functions.
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Enzyme Activity - Q&A Review
1. What are catalysts?
Catalysts are substances that reduce the activation energy of a chemical reaction, facilitating it or making it energetically viable. The catalyst increases the speed of the chemical reaction.
2. What amount of catalyst is consumed in the reaction it catalyzes?
Catalysts are not consumed in the reactions they catalyze.
3. Is there a difference between the initial and the final energy levels in catalyzed and non-catalyzed reactions?
The catalysis does not alter the energetic state of reagents and products of a chemical reaction. Only the energy necessary for the reaction to occur, i.e., the activation energy, is altered.
Enzyme Activity: activation energy graphic
4. What are enzymes? What is the importance of enzymes for living beings?
Enzymes are proteins that are catalysts of chemical reactions. From Chemistry it is known that catalysts are non-consumable substances that reduce theactivation energy necessary for a chemical reaction to occur.
Enzymes are highly specific to the reactions they catalyze. They are of vital importance for life because most chemical reactions of the cells and tissues are catalyzed by enzymes. Without enzymatic action those reactions would not occur or would not happen in the required speed for the biological processes in which they participate.
5. What is meant by substrates of enzymatic reactions?
Substrates are reagent molecules upon which enzymes act.
The enzyme has spatial binding sites for the attachment of its substrate. These sites are called activation centers of the enzyme. Substrates bind to theses centers forming the enzyme-substrate complex.
Enzyme Activity: enzyme-substrate complex
6. What are the main theoretical models that try to explain the formation of the enzyme-substrate complex?
There are two main models that explain the formation of the enzyme-substrate complex: the lock and key model and the induced fit model.
In the lock and key model the enzyme has a region with specific spatial conformation for the binding of the substrate. In the induced fit model the binding of the substrate induces a change in the spatial configuration of the enzyme for the substrate to fit.
Enzyme Activity: lock and key model induced fit model
7. How does the formation of the enzyme-substrate complex explain the reduction of the activation energy of chemical reactions?
The enzyme possibly works as a test tube within which reagents meet to form products. With the facilitation of the meeting provided by enzymes it is easier for collisions between reagents to occur and thus theactivation energy of the chemical reaction is reduced. This is one of the possible hypotheses.
8. On what structural level of the enzyme (primary, secondary, tertiary or quaternary) does the enzyme-substrate interaction depend?
The substrate binds to the enzyme in the activation centers. These are specific three-dimensional sites and thus they depend on the protein tertiary and quaternary structures. The primary and secondary structures, however, condition the other structures and so they are equally important.
9. What is the activation center of an enzyme? Is it the key or the lock of the lock and key model?
The activation center is a region of the enzyme produced by its spatial conformation to which the substrate binds. In the lock and key model the activation center is the lock and the substrate is the key.
10. Why can it be said that the enzymatic action is highly specific?
The enzymatic action is highly specific because only specific substrates of one enzyme bind to the activation center of that enzyme. Each enzyme generally catalyzes only a specific chemical reaction.
11. What happens to a denatured enzyme regarding its functionality? How can that result be explained with the help of the lock and key model?
According to the lock and key model the enzyme functionality depends entirely on the integrity of the activation center, a molecular region with specific spatial characteristics. After the denaturation the spatial conformation of the protein is modified, theactivation center is destroyed and the enzyme loses its catalytic activity.
12. What are the main factors that alter the speed of enzymatic reactions?
The main factors that change the speed of enzymatic reactions are temperature, pH and substrate concentration (quantity).
13. How does the substrate concentration affect the speed of enzymatic reactions?
Initially as substrate concentration increases, the speed of the reaction increases; this happens because free activation centers of the enzyme bind to free substrates. Once all activation centers of the available enzymes become bound to their substrates new increments of the substrate concentration will have no effect on thespeed of the reaction.
14. How does temperature affect the action of enzymes upon their substrates?
There are defined temperature ranges under which enzymes operate and there is a specific temperature level (optimum temperature) in which enzymes have maximum efficiency. Therefore temperature variations affect enzymatic activity and thespeed of the reactions they catalyze.
In addition, as proteins, enzymes can be denatured under extreme temperatures.
15. Concerning enzymatic reactions, how different are the graphic curve of the variation of the speed of a reaction as function of substrate concentration and the curve of variation of the speed of a reaction as function of temperature?
The curve of variation of speed of the enzymatic reaction as a function of growing substrate concentration is a growing curve until the point where it stabilizes due to the saturation of theactivation centers of the enzymes.
The curve of variation of speed of the enzymatic reaction as a function of growing temperature has a crescent portion and reaches a peak (the optimum temperature) then it decreases and reaches zero in the point of inactivity of the enzymes by denaturation.
16. How is the cooling of organs and tissues for medical transplants associated with the effect of temperature upon enzymatic reactions?
The molecular degradation during the decomposition of organs and tissues is catalyzed by enzymes. The cooling to adequate temperatures of some organs and tissues destined for transplantation reduces that enzyme activity and thus lessens the natural decomposition process. By the same rationale, the cooling reduces the metabolic work of cells and prevents degradation of their own structures to obtain energy. Elevation of temperature later reverts denaturation of enzymes and the organs and tissues also preserved by other specific techniques may be grafted into the receptors.
17. Does pH affect the enzyme activity?
The concentration of hydrogen ions in solution affects the enzyme activity. Each enzyme has maximal efficiency under an optimum pH.
Since pH is one of the factors for the denaturation of proteins, if an enzyme is submitted to a pH level under which it is denatured there will be no enzymatic activity.
18. Do enzymes act better under acid or basic pH?
Most enzymes act in pH between 6 and 8, a range that corresponds to the general acidic level of cells and blood. There are enzymes, however, that act only under very acid or very basic pH. So enzyme activity depends on pH interval.
In the stomach, for example, the gastric juice has a very low pH, around 2, and there the enzyme pepsin acts to intensively digest proteins. In the duodenum, pancreatic secretions increase the pH of the enteric juice for the action of other digestive enzymes, for example, trypsin.
19. Since pepsin is a gastric enzyme does it have an acid or basic optimum pH? What happens to pepsin when it passes into the duodenum?
Pepsin acts within the stomach so its optimum pH is around 2, an acid pH. When the enzyme passes into the duodenum it meets a higher pH and its enzyme activity ends.
20. What are enzyme cofactors?
Some enzymes need other associated molecules to work. These molecules are called enzyme cofactors and they can be, for example, organic ions like mineral salts, or organic molecules.
Inactive enzymes which are not bound to their cofactors are called apoenzymes. Active enzymes bound to their cofactors are called holoenzymes.
21. What is the relationship between vitamins and enzyme cofactors?
Many vitamins are enzyme cofactors that cannot be synthesized by the organism and must be obtained from the diet.
22. For the enzymatic reaction what is the effect of a substance with the same spatial conformation as an enzymatic substrate? How is this type of substance known?
Substances that “simulate” substrates can bind to the activation center of enzymes thus blocking the true substrates to bind to these enzymes and paralyzing the enzymatic reaction. Such “fake substrates” are called enzyme inhibitors.
The binding of enzyme inhibitors to enzymes can be reversible or irreversible.
Many medical drugs, for example, some antibiotics, antivirals, antineoplastics, antihypertensives and even sildenafil (trade name Viagra), are enzyme inhibitors that block enzyme activity.
23. What is the action mechanism of the antibiotic penicillin?
Penicillin, discovered by the Scottish doctor Alexander Fleming in 1928, is a drug that inhibits enzymes necessary for the synthesis of peptidoglycans, a constituent of the bacterial cell wall. With the inhibition the bacterial population stops growing because there is no new cell wall formation.
Fleming won the Nobel prize in Medicine for the discovery of penicillin.
24. What is the action mechanism of the antiretroviral drugs called protease inhibitors which are used against HIV infection?
Protease inhibitors are some of the antiretroviral drugs used to treat HIV infection. Protease is an enzyme necessary for the assembling of HIV after the synthesis of its proteins within the host cell. The protease inhibitor binds to the activation center of the enzyme blocking the formation of the enzyme-substrate complex and the enzyme activity thus impairing the viral replication.
25. What are allosteric enzymes?
Allosteric enzymes are those that have more than one activation center and to which other substances, called allosteric regulators, bind.
Allosteric regulators can be allosteric inhibitors or allosteric activators. The interaction between an allosteric enzyme and the allosteric inhibitor disallows the binding of the substrate to the enzyme. The interaction between the allosteric enzyme and the allosteric activator allows the binding of the substrate to the enzyme and sometimes increases the affinity of the enzyme for the substrate. This regulatory phenomenon of the enzyme activity is called allosterism.
Enzyme Activity: allosteric enzymes
26. What are zymogens?
Zymogens, or proenzymes, are enzymes secreted in inactive form. Under certain conditions a zymogen shifts to the active form of the enzyme. Zymogen secretions in general happen because the enzyme activity can harm the secretory tissue.
For example, the pepsinogen secreted by the stomach becomes active under acid pH turning into the enzyme pepsin. Other well-known zymogens are trypsinogen and chymotrypsinogen, enzymes that are secreted by the exocrine pancreas and which become trypsin and chymotrypsin respectively.
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DNA and RNA Review
1. What are nucleic acids? What is the historic origin of this name?
DNA and RNA, the nucleic acids, are the molecules responsible for the hereditary information that commands the protein synthesis in living beings. The name “nucleic” derives from the fact that they were discovered (by the Swiss biochemist Friedrich Miescher, in 1869) within the cell nucleus. In that time it was not known that those substances contained the hereditary information.
2. Of what units are nucleic acids constituted? What are the chemical entities that compose that unit?
Nucleic acids are formed by sequences of nucleotides.
Nucleotides are constituted by one molecule of sugar (deoxyribose in DNA and ribose in RNA) bound to one molecule of phosphate and to one nitrogen-containing base (adenine, uracil, cytosine or guanine, in RNA, and adenine, thymine, cytosine and guanine, in DNA).
Nucleic Acid Review - Image Diversity: nucleotide structure nitrogen-containing bases
3. What are pentoses? To what organic group do pentoses belong? Are nucleotides formed of only one type of pentose?
Pentoses are carbohydrates made of five carbons. Deoxyribose is the pentose that constitutes DNA nucleotides and ribose is the pentose that is part of RNA nucleotides.
4. Into which two groups can the nitrogen-containing bases that form DNA and RNA be classified? What is the criterion used in that classification?
The nitrogen-containing bases that form DNA and RNA are classified as pyrimidine and purine bases.
By the analysis of the structural formulae of those nitrogen-containing bases it is possible to realize that three of them, cytosine, thymine and uracil, have only one nitrogenized carbon ring. The others, adenine and guanine, have two nitrogenized associated carbon rings.
Nucleic Acid Review - Image Diversity: pyrimidine bases purine bases
5. Concerning the nitrogen-containing bases that participate in nucleotides, what is the difference between DNA and RNA?
In DNA nucleotides can be formed of adenine (A), thymine (T), cytosine (C) or guanine (G). In RNA nucleotides can also contain adenine (A), cytosine (C) or guanine (G), however, instead of thymine (T) there is uracil (U).
6. Which are the nucleotides “portions” that bind in the formation of nucleic acids? What is meant by the 5’ and 3’ extremities of nucleic acids?
The phosphate group of one nucleotide binds to the pentose of the other nucleotide and so on to make the polynucleotide chain.
Each extremity of a DNA or RNA chain can be distinguished from the other extremity according to their terminal chemical entity. The phosphate-ended extremity is called 5’-extremity and the pentose-ended extremity is called 3’-extremity. So DNA or RNA chains can be run along the 5’-3’ way or along the 3’-5’ way. These ways are important in several biological functions of DNA and RNA since some reactions specifically occur following one way or the other way.
7. Bacteria are prokaryotic cells, i.e., they do not have a membrane-delimited nucleus. Eukaryotes have cells with a delimited nucleus. Where in these types of cells can DNA be found?
In eukaryotic cells DNA is found within the cell nucleus. In prokaryotic cells DNA is found dispersed in the cytosol, the fluid space inside the cell.
Other DNA molecules can also be found within mitochondria and chloroplasts, specialized organelles of eukaryotic cells.
8. Who were James Watson, Francis Crick and Maurice Wilkins?
Watson (North American), Crick (British) and Wilkins (New Zealander) were the discoverers of the molecular structure of DNA, the double helix made of two polynucleotide chains paired by their nitrogen-containing bases. They won the Nobel prize in Medicine in 1962 for the discovery.
Nucleic Acid Review - Image Diversity: Watson and Crick
9. According to the Watson-Crick model how many polynucleotide chains does a DNA molecule have?
The DNA molecule is formed by two polynucleotide chains bound in antiparallel mode (5’-3’ to 3’-5’) and forming a helical structure.
Nucleic Acid Review - Image Diversity: DNA double helix
10. What is the rule for the pairing of nitrogen-containing bases in the DNA molecule? And in the RNA? Is this last question appropriate?
The rule for the pairing of nitrogen-containing bases of the polynucleotide chains that form the DNA molecule is pyrimidine base binds to purine base, under the condition that thymine (T) binds to adenine (A) andcytosine (C) binds to guanine (G).
In RNA there is no binding between nitrogen-containing bases. That is because RNA is formed of only one polynucleotide chain; differently, DNA is formed of two chains. It is therefore not correct to question base pairing in RNA.
Nucleic Acid Review - Image Diversity: DNA base pairing
11. What is the numeric relation between pyrimidine and purine bases in the DNA molecule? Is that relation valid in RNA molecules?
The DNA molecule is made of two bound polynucleotide chains that form a helical structure (the double helix). The binding of the two chains is between their nitrogen-containing bases and it always obeys the following rules: adenine (A), a purine base, binds with thymine (T), a pyrimidine base, andguanine (G), a purine base, binds to cytosine (C), a pyrimidine base. Therefore in one molecule of DNA there will be the same number of adenine (A) and thymine (T) and same number ofcytosine (C) and guanine (G). The quantities of purine and of pyrimidine bases then will also be the same in a 50% proportion for each type. The relation A = T and C = G, or A/T = C/G = 1, is called Chargaff’s relation and the pairing rules described above are known as Chargaff’s rules.
In RNA there are not two nucleotide chains. RNA is a simple chain molecule and there is no necessary proportionality of nitrogen-containing bases to form it.
12. Which type of chemical bond maintains the pairing of each chain in the DNA molecule?
To form the DNA molecule, purine bases bind to pyrimidine bases by intermolecular bonds called hydrogen bonds. Hydrogen bonds occur when there is hydrogen near one of these electronegative elements: fluorine, oxygen or nitrogen.
In such conditions hydrogen looks like having lost electrons for those elements and a very strong polarization is created. The highly positive hydrogen attracts pairs of electrons of othermolecules making a hydrogen bond.
13. What is the completing sequence of nitrogen-containing bases for a AGCCGTTAAC fragment of a DNA chain?
TCGGCAATTG.
14. What is the name of the DNA duplication process? What is the main enzyme that participates in it?
The process of copying, or duplication, of the DNA molecule is called replication. The enzyme that participates in the formation of a new DNA chain is the DNA polymerase. There are also other important enzymes in the replication process, the helicase, the gyrase and the ligase.
Nucleic Acid Review - Image Diversity: DNA replication
15. Why is it not correct to assert that DNA self-replicates?
DNA is not completely autonomous in its duplication process because the replication does not occur without enzymatic activity. So it is not entirely correct to assert that DNA self-replicates.
16. How do the two complementary nucleotide chains of the DNA facilitate the replication process of the molecule?
The fact that the DNA molecule is made of two polynucleotide chains whose nitrogen-containing bases form hydrogen bonds facilitates the duplication of the molecule. During the DNA replication, the binding of the two chains is broken and each of them serves as a template for the formation of a new nucleotide sequence along it, with the help of the enzyme DNA polymerase and obeying the pairing rule A-T, C-G. At the end of the process two double helix of DNA are produced, each made of an original template chain and of a new synthesized polynucleotide chain.
17. What are the chemical bonds of the DNA molecule that are broken for the replication process to occur?
During the DNA replication process, hydrogen bonds between nitrogen-containing bases of the polynucleotide chains are broken.
18. As a result of DNA replication two DNA molecules come into existence. Why is it not correct to assert that two “new” DNA molecules are created? What is the name given to the process concerning that fact?
During replication each chain of the DNA molecule acts by pairing new nucleotides and after the process two newly formed chains made with the union of these nucleotides appear. Then two DNAmolecules are created, each with one chain from the original molecule and one new chain formed by new nucleotides. Thus it is not entirely correct to assert that the replication produces two newmolecules of DNA. It is better to affirm that two new half-molecules are created.
For this phenomenon DNA replication is called semiconservative replication.
19. Does DNA replication occur in cell division?
Yes. DNA replication occurs in mitosis as well in meiosis.
20. One characteristic of the DNA molecule is its replication capability. What are the consequences of failures during DNA replication?
Ideally a DNA molecule should replicate in a perfect way. Sometimes however failures in the duplication occur, with alteration (deletion, addition or substitution) of one or more nucleotides in the molecule.
Those mistakes, or mutations, therefore make changes in the protein synthesis process too. For example, the production of an important protein for cells or tissues may be suppressed, new utile or inutile proteins can be created, etc. The mistake in the DNA duplication and the resulting production of altered genetic material are some of the main creative forces for the biological evolution and the diversity of species.
21. Mistakes may happen during every copying process. The same is true for DNA replication. Are there correction systems in cells that try to fix those mistakes? Under which situation are the mistakes carried only by the individual owner of the cell within which the mistake has occurred and in which situation are they transmitted to other individuals?
The cell is equipped with an enzymatic system that tries to fix mistakes of the DNA replication process. This system however is not completely efficient.
DNA replication mistakes are kept in the original individual where the failure occurred when the phenomenon affects somatic cells. If a replication mistake occurs in the formation of a germline cell (e.g., in gametes) the DNA alteration may be transmitted to the offspring of the individual.
22. Where can RNA be found within cells?
In the eukaryote cell nucleus RNA can be found dispersed in the nuclear fluid, along with DNA, and as the main constituent of the nucleolus. In cytosol (in eukaryotes or in bacteria) RNA molecules can be found free, as structural constituent of ribosomes (organelles specialized in protein synthesis) or even associated to them in the process of making proteins.
Mitochondria and chloroplasts also have their own DNA and RNA.
23. Does RNA molecule have two polynucleotide chains like DNA?
Only DNA has two polynucleotide chains. RNA is formed by just one polynucleotide chain.
Nucleic Acid Review - Image Diversity: RNA molecule
24. What is the production of RNA called and what is the enzyme that catalyzes the process?
The making of RNA from information contained in DNA is called transcription. The enzyme that catalyzes the process is the RNA polymerase.
Nucleic Acid Review - Image Diversity: RNA transcription
25. What are similarities and differences between the transcription process and the replication processes?
A DNA polynucleotide chain serves as a template in replication (DNA duplication) as well as in transcription (RNA formation). In both processes the pairing of the two polynucleotide chains of the original DNA molecule is broken by the breaking of hydrogen bonds for the chains to be exposed as templates. The reaction is catalyzed by specific enzymes in transcription and in replication.
In replication the enzyme DNA polymerase catalyzes the formation of a new polynucleotide chain using free nucleotides in solution and putting them in the new chain according to the DNA template exposed and to the rule A-T, C-G. In transcription the enzyme RNA polymerase makes a new polynucletide chain according to the DNA template exposed obeying, however, the rule A-U, C-G.
In replication the original template DNA chain is kept bound by hydrogen bonds to the newly formed DNA chain and a new DNA molecule is then created. In transcription the association between the template DNA chain and the newly formed RNA is undone and RNA constituted of only one polynucleotide chain is liberated.
26. What are the three main types of RNA? What is meant by heterogeneous RNA?
Messenger RNA, or mRNA, transfer RNA, or tRNA, and ribosomal RNA, or rRNA, are the three main types of RNA.
The newly formed RNA molecule, a precursor of mRNA, is called heterogeneous RNA (hnRNA). The heterogenous RNA bears portions called introns and portions called exons. The hnRNA is processed in many chemical steps, introns are removed and mRNA is created formed only of exons, the biologically active nucleotide sequences.
27. Concerning their biological function what is the difference between DNA and RNA?
DNA is the source of information for RNA production (transcription) and thus for protein synthesis. DNA is still the basis of heredity due to its replication capability.
The messenger RNA is the template for protein synthesis (translation). In this process tRNA and rRNA also participate since the first carries amino acids for the polypeptide chain formation and the second is a structural constituent of ribosomes (the organelles where proteins are made).
28. Is there any situation in which DNA is made based on a RNA template? What is the enzyme involved?
The process in which DNA is synthesized having as template a RNA chain is called reverse transcription. In cells infected by retroviruses (RNA viruses, like the AIDS or SARS viruses) reverse transcription occurs and DNA is made from information contained in the viral RNA.
Viral RNA within the host cell produces DNA with the help of an enzyme called reverse transcriptase. Based on that DNA the host cell then makes viral proteins, new viruses are assembled and viral replication occurs.
Nucleic Acid Review - Image Diversity: reverse transcription
29. Do the phosphate and the pentose groups give homogeneity or heterogeneity to the nucleic acid chains? What about the nitrogen-containing groups? Supported by that, which of those groups is expected to directly participate in the highly diverse and heterogeneous genetic coding, i.e., which of those groups is the basis of the information for protein production?
The phosphate and the pentose groups are the same in every nucleotide that forms the nucleic acid and so they give homogeneity to the molecule. The nitrogen-containing bases however can vary among adenine, thymine, cytosine, guanine (in DNA) and uracil (in RNA). These variations provide the heterogeneity of the nucleic acid molecule.
Homogeneous portions of a molecule seldom would store any information, by the same reason that a sequence of the same letter of the alphabet cannot make many words with different meanings. The nitrogen-containing bases, on the other hand, because they are different (four different types for RNA or DNA), can make different sequences and combinations that allow the diversity of the genetic code
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