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Biochemistr
y
Introduction
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.
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 (including glucose), 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 of glucose, 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 of glucose.
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 of chemical reactions. On the other hand, water is not good as a solvent for non-polar substances. Polarity is one of the water properties.
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, 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.
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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 (PO 4 --), the bicarbonate anion (HCO - ), the nitrate anion (NO - ) and the sulfate anion (SO - ).
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 outside the 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 of the cell membrane. Mineral salts are responsible for that voltage. The cell membrane of non-excited cell has commonly a negative inner side and
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.
Carbohydrate
s
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 C 6 H 12 O 6. 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 CH 2 OH radical. Spatial sides of hydroxyl bonds are alternated.
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
Lipids
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.
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.
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.
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.
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.
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 – NH 2 , 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 –NH 2 , (^) secondary amines, those where one hydrogen^ of NH 2 is substituted by (^) another –R, thus having two –R, and tertiary amines, those with no hydrogen bound to the nitrogen and with three – R.
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”.
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 of amino 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.
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 the peptide 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.
The tertiary protein structure is a spatial conformation additional to the secondary structure in which the alpha- helix or the beta-sheet folds itself up. The forces that keep the tertiary structure generally are interactions between the –R groups of the amino acids and between other parts of the protein and water molecules of the solution. The main types of tertiary structure of proteins are the globular proteins and the fibrous proteins.
24. What is the quaternary
structure of a protein? Do
all proteins have
quaternary structure?
The quaternary protein structure is the spatial conformation due to interactions among polypeptide chains that form the protein. Only those proteins made of two or more polypeptide chains have quaternary structure. Insulin (two chains), hemoglobin (four chains) and the immunoglobulins (antibodies, four chains) are some examples of protein having quaternary structure.
25. What is protein
denaturation? Is there any
change in the primary
structure when a protein is
denatured?
Secondary, tertiary and quaternary structures of proteins are spatial structures. Denaturation is modification in any of these spatial structures that makes the protein deficient or biologically inactive. After denaturation the primary protein structure is not affected.
26. How can denaturation be
classified regarding its
reversibility?
Protein denaturation can be a reversible or an irreversible process, i.e., it may be possible or impossible to make the protein regain its original spatial conformation.
27. What are some factors
that can lead to protein
denaturation?
Protein denaturation can be caused by temperature variation, pH change, changes in the concentration of surrounding solutes and by other processes. Most proteins denature after certain elevation of temperature or when in very acid or very basic solutions. This is one of the main reasons that it is necessary for the organisms to keep stable temperature and pH.
28. Is it expected that a
change in the primary, in the
secondary or in the tertiary
structure of a protein will
produce more functional
consequences?
Any change of the protein structure is relevant if it alters its biological activity. Changes in the primary protein structure are more important because they are modifications in the composition of the molecule and such composition determines all other structures of the protein.
29. In sickle cell anemia, a
hereditary disease, there is
substitution of one amino
acid by another in one of the
four polypeptide chains of
hemoglobin. In this case are
all of the structural levels of
the protein modified?
In sickle cell disease there is a change in the primary protein structure of one of the polypeptide chains that form hemoglobin: the amino acid glutamic acid is substituted by the amino acid valine in the β chain. The spatial conformation of the molecule in addition is also affected and modified by this primary “mistake” and the modification also creates a different (sickle) shape to the red blood cells. Modified, sickled, red blood cells sometimes aggregate and obstruct the peripheral circulation causing tissue hypoxia and the pain crisis typical of sickle cell anemia.
30. What is the difference
between essential and
natural amino acids?
Essential amino acids are those that the organism is not able to synthesize and that need to be ingested by the individual. Natural amino acids are those that are produced by the organism. There are living species that produce every amino acid they need, for example, the bacteria Escherichia coli, that does not have essential amino acids. Other species, like humans, need to obtain essential amino acids from the diet. Among the twenty different known amino acids that form proteins humans can make twelve of them and the remaining eight need to be taken from the proteins they ingest with food. The essential amino acids for humans are phenylalanine, histidine, isoleucine, lysine, methionine, threonine, tryptophane and valine.
31. What are respectively
some remarkable functions of
myosin, CD4, albumin, keratin,
immunoglobulin, reverse
transcriptase, hemoglobin and
insulin?
Myosin is a protein that when associated with actin produces a muscular contraction. CD4 is a membrane protein of some lymphocytes, the cells that are infected by HIV. Albumin is an energy storage protein and also an important regulator of the blood osmolarity.
Enzymes
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.
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 the activation 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.
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.
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 the activation 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, the activation center is destroyed and the enzyme loses its catalytic activity.
