Lecture Nucleic acids. ATP nucleic acids. §6. Nucleic acids. ATP ATP is characterized by the fact that it has a polymer structure
Lecture 4. Nucleic acids. ATPNucleic acids. To
Rice. . DNA structure
Nucleic acids include high-polymer compounds that decompose during hydrolysis into purine and pyrimidine nitrogenous bases, pentose and phosphoric acid. Nucleic acids contain carbon, hydrogen, phosphorus, oxygen and nitrogen. There are two classes of nucleic acids: ribonucleic acids (RNA) and deoxyribonucleic acids (DNA). Structure and functions of DNA. DNA molecule - heteropolymer, whose monomers are deoxyribonucleotides. The model of the spatial structure of the DNA molecule in the form of a double helix was proposed in 1953 by J. Watson and F. Crick ( Nobel Prize), to build this model they used the work of M. Wilkins, R. Franklin, E. Chargaff. The DNA molecule is formed by two polynucleotide chains, spirally twisted around each other, and together around an imaginary axis, i.e. is a double helix (exception - some DNA-containing viruses have single-stranded DNA). The diameter of the DNA double helix is 2 nm, the distance between adjacent nucleotides is 0.34 nm, and there are 10 base pairs per turn of the helix. The length of the molecule can reach several centimeters. Molecular weight - tens and hundreds of millions. The total length of the DNA of the human cell nucleus is about 2 m. In eukaryotic cells, DNA forms complexes with proteins and has a specific spatial conformation. DNA monomer - nucleotide (deoxyribonucleotide)- consists of residues of three substances: 1) a nitrogenous base, 2) a five-carbon monosaccharide (deoxyribose) and 3) phosphoric acid. The nitrogenous bases of nucleic acids belong to the classes of pyrimidines and purines. Pyrimidine bases of DNA (have one ring in their molecule) - thymine, cytosine. Purine bases (have two rings) - adenine and guanine. O
Rice. . DNA nucleotide formation
Nucleotide formation occurs in two steps. At the first stage, as a result of the condensation reaction, nucleoside is a complex of a nitrogenous base with a sugar. In the second step, the nucleoside undergoes phosphorylation. In this case, a phosphoester bond arises between the sugar residue and phosphoric acid. Thus, a nucleotide is a nucleoside linked to a phosphoric acid residue (Fig.). The name of the nucleotide is derived from the name of the corresponding base. Nucleotides and nitrogenous bases are indicated by capital letters.
nitrogenous | Name | Designation |
adenine | Adenyl | |
Guanine | Guanyl | |
Timin | thymidyl | Fig. Dinucleotide formation |
Cytosine | Cytidyl |
Rice. . DNA
Two hydrogen bonds occur between adenine and thymine, and three hydrogen bonds between guanine and cytosine. The pattern according to which the nucleotides of different DNA strands are arranged in a strictly ordered manner (adenine - thymine, guanine - cytosine) and selectively combine with each other is called the principle of complementarity.. It should be noted that J.Watson and F.Crick came to understand the principle of complementarity after reading the works of E.Chargaff. E
Rice. . Pairing of nitrogenous bases.
Chargaff, having studied a huge number of samples of tissues and organs of various organisms, found that in any DNA fragment the content of guanine residues always exactly corresponds to the content of cytosine, and adenine to thymine ("Chargaff's rule"), but he could not explain this fact. This provision is called "Chargaff's rule": A + GA = T; G \u003d C or --- \u003d 1 C + TI It follows from the principle of complementarity that the nucleotide sequence of one chain determines the nucleotide sequence of another. DNA chains antiparallel(opposite), that is, the nucleotides of different chains are located in opposite directions, and, therefore, opposite the 3 "end of one chain is the 5" end of the other. The DNA molecule is sometimes compared to spiral staircase. The "railing" of this ladder is the sugar-phosphate backbone (alternating residues of deoxyribose and phosphoric acid); “steps” are complementary nitrogenous bases. The function of DNA is the storage of hereditary information. DNA doubling.DNA replication- the process of self-doubling, the main property of the DNA molecule. Replication belongs to the category of matrix synthesis reactions and involves enzymes. Under the action of enzymes, the DNA molecule unwinds and around each strand acting as a template, a new strand is completed according to the principles of complementarity and antiparallelism. Thus, in each daughter DNA, one strand is the parent strand, and the second strand is newly synthesized, this method of synthesis is called semi-conservative The "building material" and energy source for replication are deoxyribonucleoside triphosphates (ATP, TTP, GTP, CTP) containing three phosphoric acid residues. When deoxyribonucleoside triphosphates are included in the polynucleotide chain, two terminal phosphoric acid residues are cleaved off, and the released energy is used to form a phosphodiester bond between nucleotides. In
Fig. DNA replication.
The following enzymes take part in replication: 1) helicases ("unwind" DNA); 2) destabilizing proteins; 3) DNA topoisomerases (cut DNA); 4) DNA polymerases (select deoxyribonucleoside triphosphates and complementarily attach them to the DNA template chain); 5) RNA primases (form RNA primers, primers); 6) DNA ligases (sew DNA fragments). With the help of helicases, DNA is untwisted in certain regions, single-stranded regions of DNA are bound by destabilizing proteins, and a replication fork is formed. With a discrepancy of 10 pairs of nucleotides (one turn of the helix), the DNA molecule must complete a complete revolution around its axis. To prevent this rotation, DNA topoisomerase cuts one strand of DNA, which allows it to rotate around the second strand. DNA polymerase can only attach a nucleotide to the 3" carbon of the deoxyribose of the previous nucleotide, so this enzyme is able to move along template DNA in only one direction: from the 3" end to the 5" end of this template DNA. Since the chains in maternal DNA are antiparallel , then on its different chains the assembly of daughter polynucleotide chains occurs in different ways and in opposite directions. leading. On the chain "5"-3"" - intermittently, in fragments ( fragments of Okazaki), which, after completion of replication by DNA ligases, are fused into one strand; this child chain will be called lagging(lagging behind). A feature of DNA polymerase is that it can only start its work with a "seed" (primer). The role of primers is performed by short RNA sequences formed with the participation of the enzyme RNA primases and paired with matrix DNA. After the assembly of polynucleotide chains is completed, RNA primers are removed and replaced with DNA nucleotides by another DNA polymerase. Replication proceeds similarly in prokaryotes and eukaryotes. The rate of DNA synthesis in prokaryotes is an order of magnitude higher (1000 nucleotides per second) than in eukaryotes (100 nucleotides per second). Replication begins simultaneously in several regions of the DNA molecule that have a specific nucleotide sequence and are called origins(English origin - the beginning). A piece of DNA from one origin of replication to another forms a unit of replication - replicon.
Rice. . DNA replication enzymes:
1 - helicases; 2 - destabilizing proteins; 3 – leading strand of DNA; 4 - synthesis of the Okazaki fragment; 5 - the primer is replaced by DNA nucleotides and the fragments are linked by ligases; 6 - DNA polymerase; 7 - RNA primase, synthesizes RNA primer; 8 - RNA primer; 9 – Okazaki fragment; 10 - ligase that links Okazaki fragments; 11 – topoisomer cutting one of the DNA strands.
R
Rice. DNA replicons
Eplication occurs before cell division. Thanks to this ability of DNA, the transfer of hereditary information from the mother cell to the daughter cells is carried out. Repair(“repair”) is the process of repairing damage to the DNA nucleotide sequence. It is carried out by special enzyme systems of the cell (repair enzymes). The following steps can be distinguished in the process of DNA structure repair: 1) DNA-repairing nucleases recognize and remove the damaged area, resulting in a gap in the DNA chain; 2) DNA polymerase fills this gap by copying information from the second (“good”) strand; 3) DNA ligase "crosslinks" the nucleotides, completing the repair.
Rice. . RNA structure
Ribonucleic acids RNA is a heteropolymer molecule whose monomers are ribonucleotides. Unlike DNA, RNA is formed not by two, but by one polynucleotide chain (exception - some RNA-containing viruses have double-stranded RNA). RNA nucleotides are able to form hydrogen bonds with each other, but these are intra-, not inter-strand bonds. RNA chains are much shorter than DNA chains. The RNA monomer - nucleotide (ribonucleotide) - consists of residues of three substances: 1) a nitrogenous base, 2) a five-carbon monosaccharide (ribose) and 3) phosphoric acid. The nitrogenous bases of RNA also belong to the classes of pyrimidines and purines. Pyrimidine bases of RNA uracil, cytosine, purine bases - adenine and guanine. AT
Rice. . tRNA
There are three types of RNA: 1) information (matrix) RNA - mRNA (mRNA), 2) transfer RNA - tRNA, 3) ribosomal RNA - rRNA. All types of RNA are unbranched polynucleotides, have a specific spatial conformation and take part in the processes of protein synthesis. Information about the structure of all types of RNA is stored in DNA. The process of synthesis of RNA on a DNA template is called transcription. Transfer RNAs- usually contain from 76 to 85 nucleotides; molecular weight - 25,000-30,000. tRNA accounts for about 10% of the total RNA content in the cell. tRNA is responsible for the transport of amino acids to the site of protein synthesis, to ribosomes. About 30 types of tRNA are found in the cell, each of them has a nucleotide sequence characteristic only for it. However, all tRNAs have several intramolecular complementary regions, due to which tRNAs acquire a clover-leaf conformation. – formation of a compact structure due to the interaction of spiralized sections of the secondary structure. Any tRNA has a loop for contact with the ribosome, an anticodon loop with an anticodon, a loop for contact with the enzyme, and an acceptor stem. The amino acid is attached to the 3 "end of the acceptor stem. Anticodon - three nucleotides that "recognize" the mRNA codon. It should be emphasized that a particular tRNA can transport a strictly defined amino acid corresponding to its anticodon. -synthetase. Ribosomal RNA- contain 3,000-5,000 nucleotides. rRNA accounts for 80-85% of the total RNA content in the cell. In combination with ribosomal proteins, rRNA forms ribosomes - organelles that carry out protein synthesis. In eukaryotic cells, rRNA synthesis occurs in the nucleolus. Information RNA varied in nucleotide content and molecular weight (up to 30,000 nucleotides). The share of mRNA accounts for up to 5% of the total RNA content in the cell. The functions of mRNA are the transfer of genetic information from DNA to ribosomes; a matrix for the synthesis of a protein molecule; determination of the amino acid sequence of the primary structure of the protein molecule. ATP, OVER + , NADP + , FAD.Adenosine triphosphoric acid (ATP) - a universal source and main energy accumulator in living cells. ATP is found in all plant and animal cells. The amount of ATP averages 0.04% (of the raw mass of the cell), the largest amount of ATP (0.2-0.5%) is found in skeletal muscles. In the cell, the ATP molecule is consumed within one minute after its formation. In humans, an amount of ATP equal to body weight is formed and destroyed every 24 hours..ATP is a mononucleotide consisting of residues of a nitrogenous base (adenine), ribose, and three residues of phosphoric acid. Since ATP contains not one, but three phosphoric acid residues, it belongs to ribonucleoside triphosphate.For most types of work occurring in cells, the energy of ATP hydrolysis is used. At the same time, when the terminal residue of phosphoric acid is cleaved off, ATP passes into ADP (adenosine diphosphoric acid), when the second phosphoric acid residue is cleaved off, into AMP (adenosine monophosphoric acid). Exit free energy when splitting off both the terminal and the second phosphoric acid residues, it is about 30.6 kJ / mol. Cleavage of the third phosphate group is accompanied by the release of only 13.8 kJ/mol. The bonds between the terminal and the second, second and first residues of phosphoric acid are called macroergic(high-energy). ATP reserves are constantly replenished. In the cells of all organisms, ATP synthesis occurs in the process phosphorylation, i.e. addition of phosphoric acid to ADP. Phosphorylation occurs with different intensity during respiration (mitochondria), glycolysis (cytoplasm), photosynthesis (chloroplasts).
Rice. Hydrolysis of ATP
ATP is the main link between processes accompanied by the release and accumulation of energy, and processes that require energy. In addition, ATP, along with other ribonucleoside triphosphates (GTP, CTP, UTP), is a substrate for RNA synthesis. In addition to ATP, there are other molecules with macroergic bonds - UTP (uridine triphosphoric acid), GTP (guanosine triphosphoric acid), CTP (cytidine triphosphoric acid), energy which are used for the biosynthesis of protein (GTP), polysaccharides (UTP), phospholipids (CTP). But all of them are formed due to the energy of ATP. In addition to mononucleotides, dinucleotides (NAD +, NADP +, FAD), belonging to the group of coenzymes (organic molecules that remain connected with the enzyme only during the reaction), play an important role in metabolic reactions. NAD + (nicotinamide adenine dinucleotide), NADP + (nicotinamide adenine dinucleotide phosphate) are dinucleotides containing two nitrogenous bases - adenine and nicotinic acid amide - a derivative of vitamin PP), two ribose residues and two phosphoric acid residues (Fig. .). If ATP is a universal source of energy, then ABOVE + and NADP + – universal acceptors, and their restored forms - NADH and NADPH – universal donors reduction equivalents (two electrons and one proton). The nitrogen atom, which is part of the nicotinic acid amide residue, is tetravalent and carries a positive charge ( ABOVE + ). This nitrogenous base easily attaches two electrons and one proton (i.e., is reduced) in those reactions in which, with the participation of dehydrogenase enzymes, two hydrogen atoms break off from the substrate (the second proton goes into solution): Substrate-H 2 + NAD + substrate + NADH + H +
Rice. . The structure of the molecule of dinucleotides NAD + and NADP +.
A - attachment of a phosphate group to a ribose residue in the NAD molecule. B - the attachment of two electrons and one proton (H - anion) to NAD +.
In reverse reactions, enzymes, oxidizing NADH or NADPH, restore substrates by attaching hydrogen atoms to them (the second proton comes from solution). FAD - flavin adenine dinucleotide- a derivative of vitamin B 2 (riboflavin) is also a cofactor of dehydrogenases, but FAD attaches two protons and two electrons, recovering to FADH 2 .Key terms and concepts 1. DNA nucleotide. 2. Purine and pyrimidine nitrogenous bases. 3. Antiparallelism of DNA nucleotide chains. 4. Complementarity. 5. Semi-conservative mode of DNA replication. 6. Leading and lagging strands of DNA nucleotides. 7. Replicon. 8. Reparation. 9. RNA nucleotide. 10. ATP, ADP, AMP. 11. OVER +, NADP +. 12. FAD. Essential Review Questions
The joining of DNA nucleotides into one strand.
Connection of polynucleotide chains of DNA with each other.
DNA dimensions: length, diameter, length of one turn, distance between nucleotides.
Chargaff's rules, the significance of the work of D. Watson and F. Crick.
DNA replication. Enzymes that ensure replication: helicases, topoisomerases, primases, DNA polymerases; ligases.
The structure of RNA.
Types of RNA, their number, size and function.
characteristics of ATP.
Characteristics of NAD +, NADP +, FAD.
Nucleic acids(from lat. nucleus - nucleus) - acids, first discovered in the study of the nuclei of leukocytes; were discovered in 1868 by I.F. Miescher, Swiss biochemist. biological significance nucleic acids - storage and transmission of hereditary information; they are necessary to sustain life and to reproduce it.
Nucleic acids
The DNA nucleotide and the RNA nucleotide have similarities and differences.
The structure of the DNA nucleotide
The structure of the RNA nucleotide
The DNA molecule is a double helix strand.
An RNA molecule is a single strand of nucleotides, similar in structure to a single strand of DNA. Only instead of deoxyribose, RNA includes another carbohydrate - ribose (hence the name), and instead of thymine - uracil.
Two strands of DNA are connected to each other by hydrogen bonds. In this case, an important pattern is observed: opposite the nitrogenous base adenine A in one chain is the nitrogenous base thymine T in the other chain, and cytosine C is always located opposite the guanine G. These base pairs are called complementary pairs.
In this way, principle of complementarity(from lat. complementum - addition) is that each nitrogenous base included in the nucleotide corresponds to another nitrogenous base. There are strictly defined pairs of bases (A - T, G - C), these pairs are specific. There are three hydrogen bonds between guanine and cytosine, and between adenine and thymine, two hydrogen bonds occur in the DNA nucleotide, and in RNA, two hydrogen bonds occur between adenine and uracil.
Hydrogen bonds between nitrogenous bases of nucleotides
G ≡ C G ≡ C
As a result, in any organism, the number of adenyl nucleotides is equal to the number of thymidyl, and the number of guanyl nucleotides is equal to the number of cytidyl. Due to this property, the sequence of nucleotides in one chain determines their sequence in another. This ability to selectively combine nucleotides is called complementarity, and this property underlies the formation of new DNA molecules based on the original molecule (replication, i.e. doubling).
Thus, the quantitative content of nitrogenous bases in DNA is subject to certain rules:
1) The sum of adenine and guanine is equal to the sum of cytosine and thymine A + G = C + T.
2) The sum of adenine and cytosine is equal to the sum of guanine and thymine A + C = G + T.
3) The amount of adenine is equal to the amount of thymine, the amount of guanine is equal to the amount of cytosine A = T; G = C.
When conditions change, DNA, like proteins, can undergo denaturation, which is called melting.
DNA has unique properties: the ability to self-doubling (replication, reduplication) and the ability to self-repair (repair). replication ensures the exact reproduction in the daughter molecules of the information that was recorded in the parent molecule. But sometimes errors occur during the replication process. The ability of a DNA molecule to correct errors that occur in its chains, that is, to restore the correct sequence of nucleotides, is called reparations.
DNA molecules are found mainly in the nuclei of cells and in a small amount in mitochondria and plastids - chloroplasts. DNA molecules are carriers of hereditary information.
Structure, functions and localization in the cell. There are three types of RNA. The names are associated with the functions performed:
Comparative characteristics nucleic acids
Adenosine phosphoric acids - a denosine triphosphoric acid (ATP), a denosine diphosphoric acid (ADP), a denosine monophosphoric acid (AMP).
The cytoplasm of every cell, as well as mitochondria, chloroplasts and nuclei, contains adenosine triphosphate (ATP). It supplies energy for most of the reactions that take place in the cell. With the help of ATP, the cell synthesizes new molecules of proteins, carbohydrates, fats, carries out active transport substances, the beating of flagella and cilia.
ATP is similar in structure to the adenine nucleotide that is part of RNA, only instead of one phosphoric acid, ATP contains three phosphoric acid residues.
The structure of the ATP molecule:
The unstable chemical bonds that connect the phosphoric acid molecules in ATP are very rich in energy. When these bonds are broken, energy is released, which is used by each cell to ensure vital processes:
ATP ADP + P + E
ADP AMP + F + E,
where F is phosphoric acid H3PO4, E is the released energy.
Energy-rich chemical bonds in ATP between phosphoric acid residues are called macroergic bonds. The splitting of one molecule of phosphoric acid is accompanied by the release of energy - 40 kJ.
ATP is formed from ADP and inorganic phosphate due to the energy released during oxidation organic matter and during photosynthesis. This process is called phosphorylation.
In this case, at least 40 kJ / mol of energy must be expended, which is accumulated in macroergic bonds. Consequently, the main significance of the processes of respiration and photosynthesis is determined by the fact that they supply energy for the synthesis of ATP, with the participation of which most of the work in the cell is performed.
ATP is extremely rapidly updated. In humans, for example, each ATP molecule is broken down and rebuilt 2,400 times a day, so that its average lifespan is less than 1 minute. ATP synthesis is carried out mainly in mitochondria and chloroplasts (partially in the cytoplasm). The ATP formed here is sent to those parts of the cell where there is a need for energy.
ATP plays an important role in cell bioenergetics: it performs one of the most important functions - an energy store, it is a universal biological energy accumulator.
The most important substance in the cells of living organisms is adenosine triphosphate or adenosine triphosphate. If we enter the abbreviation of this name, we get ATP (eng. ATP). This substance belongs to the group of nucleoside triphosphates and plays a leading role in the metabolic processes in living cells, being an indispensable source of energy for them.
In contact with
The discoverers of ATP were the biochemists of the Harvard School of Tropical Medicine - Yellapragada Subbarao, Karl Loman and Cyrus Fiske. The discovery occurred in 1929 and became a major milestone in the biology of living systems. Later, in 1941, the German biochemist Fritz Lipmann found that ATP in cells is the main energy carrier.
The structure of ATP
This molecule has a systematic name, which is written as follows: 9-β-D-ribofuranosyladenine-5'-triphosphate, or 9-β-D-ribofuranosyl-6-amino-purine-5'-triphosphate. What compounds are in ATP? Chemically, it is the triphosphate ester of adenosine - derivative of adenine and ribose. This substance is formed by the connection of adenine, which is a purine nitrogenous base, with the 1'-carbon of ribose using a β-N-glycosidic bond. The α-, β-, and γ-molecules of phosphoric acid are then sequentially attached to the 5'-carbon of the ribose.
Thus, the ATP molecule contains compounds such as adenine, ribose, and three phosphoric acid residues. ATP is a special compound containing bonds that release a large number of energy. Such bonds and substances are called macroergic. During the hydrolysis of these bonds of the ATP molecule, an amount of energy from 40 to 60 kJ / mol is released, while this process is accompanied by the elimination of one or two phosphoric acid residues.
This is how these chemical reactions are written:
- one). ATP + water → ADP + phosphoric acid + energy;
- 2). ADP + water → AMP + phosphoric acid + energy.
The energy released during these reactions is used in further biochemical processes that require certain energy inputs.
The role of ATP in a living organism. Its functions
What is the function of ATP? First of all, energy. As mentioned above, the main role of adenosine triphosphate is the energy supply of biochemical processes in a living organism. This role is due to the fact that, due to the presence of two high-energy bonds, ATP acts as an energy source for many physiological and biochemical processes that require large energy costs. Such processes are all reactions of the synthesis of complex substances in the body. This is, first of all, the active transfer of molecules through cell membranes, including participation in the creation of an intermembrane electrical potential, and the implementation of muscle contraction.
In addition to the above, we list a few more, no less important functions of ATP, such as:
How is ATP formed in the body?
Synthesis of adenosine triphosphoric acid is ongoing, because the body always needs energy for normal life. At any given moment, there is very little of this substance - about 250 grams, which are an "emergency reserve" for a "rainy day". During illness, there is an intensive synthesis of this acid, because a lot of energy is required for the functioning of the immune and excretory systems, as well as the body's thermoregulation system, which is necessary to effectively combat the onset of the disease.
Which cell has the most ATP? These are cells of muscular and nervous tissues, since energy exchange processes are most intensive in them. And this is obvious, because the muscles are involved in the movement, which requires the contraction of muscle fibers, and the neurons transmit electrical impulses, without which the work of all body systems is impossible. Therefore, it is so important for the cell to maintain an unchanged and high level adenosine triphosphate.
How can adenosine triphosphate molecules be formed in the body? They are formed by the so-called phosphorylation of ADP (adenosine diphosphate). This chemical reaction looks like this:
ADP + phosphoric acid + energy→ATP + water.
Phosphorylation of ADP occurs with the participation of such catalysts as enzymes and light, and is carried out in one of three ways:
Both oxidative and substrate phosphorylation use the energy of substances oxidized in the course of such synthesis.
Conclusion
Adenosine triphosphoric acid is the most frequently updated substance in the body. How long does an adenosine triphosphate molecule live on average? In the human body, for example, its life span is less than one minute, so one molecule of such a substance is born and decays up to 3000 times a day. Amazingly, during the day the human body synthesizes about 40 kg of this substance! So great is the need for this "internal energy" for us!
The whole cycle of synthesis and further use of ATP as an energy fuel for metabolic processes in the organism of a living being is the very essence of energy metabolism in this organism. Thus, adenosine triphosphate is a kind of "battery" that ensures the normal functioning of all cells of a living organism.
To nucleic acids include high-polymer compounds that decompose during hydrolysis into purine and pyrimidine bases, pentose and phosphoric acid. Nucleic acids contain carbon, hydrogen, phosphorus, oxygen and nitrogen. There are two classes of nucleic acids: ribonucleic acids (RNA) and deoxyribonucleic acids (DNA).
Structure and functions of DNA
DNA- a polymer whose monomers are deoxyribonucleotides. The model of the spatial structure of the DNA molecule in the form of a double helix was proposed in 1953 by J. Watson and F. Crick (to build this model, they used the work of M. Wilkins, R. Franklin, E. Chargaff).
DNA molecule formed by two polynucleotide chains, spirally twisted around each other and together around an imaginary axis, i.e. is a double helix (exception - some DNA-containing viruses have single-stranded DNA). The diameter of the DNA double helix is 2 nm, the distance between adjacent nucleotides is 0.34 nm, and there are 10 pairs of nucleotides per turn of the helix. The length of the molecule can reach several centimeters. Molecular weight - tens and hundreds of millions. The total length of DNA in the human cell nucleus is about 2 m. In eukaryotic cells, DNA forms complexes with proteins and has a specific spatial conformation.
DNA monomer - nucleotide (deoxyribonucleotide)- consists of residues of three substances: 1) a nitrogenous base, 2) a five-carbon monosaccharide (pentose) and 3) phosphoric acid. The nitrogenous bases of nucleic acids belong to the classes of pyrimidines and purines. Pyrimidine bases of DNA(have one ring in their molecule) - thymine, cytosine. Purine bases(have two rings) - adenine and guanine.
The monosaccharide of the DNA nucleotide is represented by deoxyribose.
The name of the nucleotide is derived from the name of the corresponding base. Nucleotides and nitrogenous bases are indicated by capital letters.
nitrogenous base | Name of the nucleotide | Designation |
---|---|---|
adenine | Adenyl | A (A) |
Guanine | Guanyl | G (G) |
Timin | thymidyl | T(T) |
Cytosine | Cytidyl | C (C) |
A polynucleotide chain is formed as a result of nucleotide condensation reactions. In this case, between the 3 "-carbon of the deoxyribose residue of one nucleotide and the phosphoric acid residue of the other, phosphoether bond(belongs to the category of strong covalent bonds). One end of the polynucleotide chain ends with a 5 "carbon (it is called the 5" end), the other ends with a 3 "carbon (3" end).
Against one chain of nucleotides is a second chain. The arrangement of nucleotides in these two chains is not random, but strictly defined: thymine is always located opposite the adenine of one chain in the other chain, and cytosine is always located opposite guanine, two hydrogen bonds arise between adenine and thymine, three hydrogen bonds between guanine and cytosine. The pattern according to which the nucleotides of different strands of DNA are strictly ordered (adenine - thymine, guanine - cytosine) and selectively combine with each other is called the principle of complementarity. It should be noted that J. Watson and F. Crick came to understand the principle of complementarity after reading the works of E. Chargaff. E. Chargaff, having studied a huge number of samples of tissues and organs of various organisms, found that in any DNA fragment the content of guanine residues always exactly corresponds to the content of cytosine, and adenine to thymine ( "Chargaff's rule"), but he could not explain this fact.
From the principle of complementarity, it follows that the nucleotide sequence of one chain determines the nucleotide sequence of another.
DNA strands are antiparallel (opposite), i.e. nucleotides of different chains are located in opposite directions, and, therefore, opposite the 3 "end of one chain is the 5" end of the other. The DNA molecule is sometimes compared to a spiral staircase. The "railing" of this ladder is the sugar-phosphate backbone (alternating residues of deoxyribose and phosphoric acid); "steps" are complementary nitrogenous bases.
Function of DNA- storage and transmission of hereditary information.
Replication (reduplication) of DNA
- the process of self-doubling, the main property of the DNA molecule. Replication belongs to the category of matrix synthesis reactions and involves enzymes. Under the action of enzymes, the DNA molecule unwinds, and around each strand acting as a template, a new strand is completed according to the principles of complementarity and antiparallelism. Thus, in each daughter DNA, one strand is the parent strand, and the second strand is newly synthesized. This kind of synthesis is called semi-conservative.
The "building material" and source of energy for replication are deoxyribonucleoside triphosphates(ATP, TTP, GTP, CTP) containing three phosphoric acid residues. When deoxyribonucleoside triphosphates are included in the polynucleotide chain, two terminal residues of phosphoric acid are cleaved off, and the released energy is used to form a phosphodiester bond between nucleotides.
The following enzymes are involved in replication:
- helicases ("unwind" DNA);
- destabilizing proteins;
- DNA topoisomerases (cut DNA);
- DNA polymerases (select deoxyribonucleoside triphosphates and complementarily attach them to the DNA template chain);
- RNA primases (form RNA primers, primers);
- DNA ligases (sew DNA fragments together).
With the help of helicases, DNA is untwisted in certain regions, single-stranded DNA regions are bound by destabilizing proteins, and replication fork. With a discrepancy of 10 pairs of nucleotides (one turn of the helix), the DNA molecule must complete a complete revolution around its axis. To prevent this rotation, DNA topoisomerase cuts one DNA strand, allowing it to rotate around the second strand.
DNA polymerase can only attach a nucleotide to the 3" carbon of the deoxyribose of the previous nucleotide, so this enzyme is able to move along template DNA in only one direction: from the 3" end to the 5" end of this template DNA. Since the chains in maternal DNA are antiparallel , then on its different chains the assembly of the daughter polynucleotide chains occurs in different ways and in opposite directions. On the 3 "–5" chain, the synthesis of the daughter polynucleotide chain proceeds without interruption; this daughter chain will be called leading. On the chain 5 "–3" - intermittently, in fragments ( fragments of Okazaki), which, after completion of replication by DNA ligases, are fused into one strand; this child chain will be called lagging (lagging behind).
A feature of DNA polymerase is that it can start its work only with "seeds" (primer). The role of "seeds" is performed by short RNA sequences formed with the participation of the RNA primase enzyme and paired with template DNA. RNA primers are removed after the completion of the assembly of polynucleotide chains.
Replication proceeds similarly in prokaryotes and eukaryotes. The rate of DNA synthesis in prokaryotes is an order of magnitude higher (1000 nucleotides per second) than in eukaryotes (100 nucleotides per second). Replication begins simultaneously in several regions of the DNA molecule. A piece of DNA from one origin of replication to another forms a unit of replication - replicon.
Replication occurs before cell division. Thanks to this ability of DNA, the transfer of hereditary information from the mother cell to the daughter cells is carried out.
Reparation ("repair")
reparations is the process of repairing damage to the nucleotide sequence of DNA. It is carried out by special enzyme systems of the cell ( repair enzymes). The following steps can be distinguished in the process of DNA structure repair: 1) DNA-repairing nucleases recognize and remove the damaged area, resulting in a gap in the DNA chain; 2) DNA polymerase fills this gap by copying information from the second (“good”) strand; 3) DNA ligase “crosslinks” the nucleotides, completing the repair.
Three repair mechanisms have been studied the most: 1) photoreparation, 2) excise or pre-replicative repair, 3) post-replicative repair.
Changes in the structure of DNA occur constantly in the cell under the influence of reactive metabolites, ultraviolet radiation, heavy metals and their salts, etc. Therefore, defects in repair systems increase the rate of mutation processes and are the cause of hereditary diseases (xeroderma pigmentosa, progeria, etc.).
Structure and functions of RNA
is a polymer whose monomers are ribonucleotides. Unlike DNA, RNA is formed not by two, but by one polynucleotide chain (exception - some RNA-containing viruses have double-stranded RNA). RNA nucleotides are capable of forming hydrogen bonds with each other. RNA chains are much shorter than DNA chains.
RNA monomer - nucleotide (ribonucleotide)- consists of residues of three substances: 1) a nitrogenous base, 2) a five-carbon monosaccharide (pentose) and 3) phosphoric acid. The nitrogenous bases of RNA also belong to the classes of pyrimidines and purines.
The pyrimidine bases of RNA are uracil, cytosine, and the purine bases are adenine and guanine. The RNA nucleotide monosaccharide is represented by ribose.
Allocate three types of RNA: 1) informational(matrix) RNA - mRNA (mRNA), 2) transport RNA - tRNA, 3) ribosomal RNA - rRNA.
All types of RNA are unbranched polynucleotides, have a specific spatial conformation and take part in the processes of protein synthesis. Information about the structure of all types of RNA is stored in DNA. The process of RNA synthesis on a DNA template is called transcription.
Transfer RNAs usually contain 76 (from 75 to 95) nucleotides; molecular weight - 25,000–30,000. The share of tRNA accounts for about 10% of the total RNA content in the cell. tRNA functions: 1) transport of amino acids to the site of protein synthesis, to ribosomes, 2) translational mediator. About 40 types of tRNA are found in the cell, each of them has a nucleotide sequence characteristic only for it. However, all tRNAs have several intramolecular complementary regions, due to which tRNAs acquire a conformation that resembles a clover leaf in shape. Any tRNA has a loop for contact with the ribosome (1), an anticodon loop (2), a loop for contact with the enzyme (3), an acceptor stem (4), and an anticodon (5). The amino acid is attached to the 3' end of the acceptor stem. Anticodon- three nucleotides that "recognize" the mRNA codon. It should be emphasized that a particular tRNA can transport a strictly defined amino acid corresponding to its anticodon. The specificity of the connection of amino acids and tRNA is achieved due to the properties of the enzyme aminoacyl-tRNA synthetase.
Ribosomal RNA contain 3000–5000 nucleotides; molecular weight - 1,000,000–1,500,000. rRNA accounts for 80–85% of the total RNA content in the cell. In combination with ribosomal proteins, rRNA forms ribosomes - organelles that carry out protein synthesis. In eukaryotic cells, rRNA synthesis occurs in the nucleolus. rRNA functions: 1) a necessary structural component of ribosomes and, thus, ensuring the functioning of ribosomes; 2) ensuring the interaction of the ribosome and tRNA; 3) initial binding of the ribosome and the mRNA initiator codon and determination of the reading frame, 4) formation of the active center of the ribosome.
Information RNA varied in nucleotide content and molecular weight (from 50,000 to 4,000,000). The share of mRNA accounts for up to 5% of the total RNA content in the cell. Functions of mRNA: 1) transfer of genetic information from DNA to ribosomes, 2) a matrix for the synthesis of a protein molecule, 3) determination of the amino acid sequence of the primary structure of a protein molecule.
The structure and functions of ATP
Adenosine triphosphoric acid (ATP) is a universal source and main accumulator of energy in living cells. ATP is found in all plant and animal cells. The amount of ATP averages 0.04% (of the raw mass of the cell), the largest amount of ATP (0.2–0.5%) is found in skeletal muscles.
ATP consists of residues: 1) a nitrogenous base (adenine), 2) a monosaccharide (ribose), 3) three phosphoric acids. Since ATP contains not one, but three residues of phosphoric acid, it belongs to ribonucleoside triphosphates.
For most types of work occurring in cells, the energy of ATP hydrolysis is used. At the same time, when the terminal residue of phosphoric acid is cleaved, ATP is converted into ADP (adenosine diphosphoric acid), when the second phosphoric acid residue is cleaved, it becomes AMP (adenosine monophosphoric acid). The yield of free energy during the elimination of both the terminal and the second residues of phosphoric acid is 30.6 kJ each. Cleavage of the third phosphate group is accompanied by the release of only 13.8 kJ. The bonds between the terminal and the second, second and first residues of phosphoric acid are called macroergic (high-energy).
ATP reserves are constantly replenished. In the cells of all organisms, ATP synthesis occurs in the process of phosphorylation, i.e. addition of phosphoric acid to ADP. Phosphorylation occurs with different intensity during respiration (mitochondria), glycolysis (cytoplasm), photosynthesis (chloroplasts).
ATP is the main link between processes accompanied by the release and accumulation of energy, and processes that require energy. In addition, ATP, along with other ribonucleoside triphosphates (GTP, CTP, UTP), is a substrate for RNA synthesis.
Continuation. See No. 11, 12, 13, 14, 15, 16/2005
Biology lessons in science classes
Advanced Planning, Grade 10
Lesson 19
Equipment: tables on general biology, a diagram of the structure of the ATP molecule, a diagram of the relationship between plastic and energy exchanges.
I. Knowledge Test
Conducting a biological dictation "Organic compounds of living matter"
The teacher reads the theses under the numbers, the students write down in the notebook the numbers of those theses that are suitable in content to their version.
Option 1 - proteins.
Option 2 - carbohydrates.
Option 3 - lipids.
Option 4 - nucleic acids.
1. In its pure form, they consist only of C, H, O atoms.
2. In addition to C, H, O atoms, they contain N and usually S atoms.
3. In addition to the C, H, O atoms, they contain N and P atoms.
4. They have a relatively small molecular weight.
5. The molecular weight can be from thousands to several tens and hundreds of thousands of daltons.
6. The largest organic compounds with a molecular weight of up to several tens and hundreds of millions of daltons.
7. They have different molecular weights - from very small to very high, depending on whether the substance is a monomer or a polymer.
8. Consist of monosaccharides.
9. Consist of amino acids.
10. Consist of nucleotides.
11. They are esters of higher fatty acids.
12. Basic structural unit: "nitrogenous base - pentose - phosphoric acid residue".
13. Basic structural unit: "amino acids".
14. Basic structural unit: "monosaccharide".
15. Basic structural unit: "glycerol-fatty acid".
16. Polymer molecules are built from the same monomers.
17. Polymer molecules are built from similar, but not exactly identical, monomers.
18. Are not polymers.
19. They perform almost exclusively energy, construction and storage functions, in some cases - protective.
20. In addition to energy and construction, they perform catalytic, signal, transport, motor and protective functions;
21. They store and transfer the hereditary properties of the cell and the body.
Option 1 – 2; 5; 9; 13; 17; 20.
Option 2 – 1; 7; 8; 14; 16; 19.
Option 3 – 1; 4; 11; 15; 18; 19.
Option 4– 3; 6; 10; 12; 17; 21.
II. Learning new material
1. The structure of adenosine triphosphoric acid
In addition to proteins, nucleic acids, fats and carbohydrates, a large number of other organic compounds are synthesized in living matter. Among them, an important role in the bioenergetics of the cell is played by adenosine triphosphate (ATP). ATP is found in all plant and animal cells. In cells, adenosine triphosphoric acid is most often present in the form of salts called adenosine triphosphates. The amount of ATP fluctuates and averages 0.04% (on average there are about 1 billion ATP molecules in a cell). The largest amount of ATP is found in skeletal muscles (0.2–0.5%).
The ATP molecule consists of a nitrogenous base - adenine, pentose - ribose and three residues of phosphoric acid, i.e. ATP is a special adenyl nucleotide. Unlike other nucleotides, ATP contains not one, but three phosphoric acid residues. ATP refers to macroergic substances - substances containing a large amount of energy in their bonds.
Spatial model (A) and structural formula (B) of the ATP molecule
From the composition of ATP under the action of ATPase enzymes, a residue of phosphoric acid is cleaved off. ATP has a strong tendency to detach its terminal phosphate group:
ATP 4– + H 2 O ––> ADP 3– + 30.5 kJ + Fn,
because this leads to the disappearance of the energetically unfavorable electrostatic repulsion between neighboring negative charges. The resulting phosphate is stabilized by the formation of energetically favorable hydrogen bonds with water. The charge distribution in the ADP + Fn system becomes more stable than in ATP. As a result of this reaction, 30.5 kJ are released (when a conventional covalent bond is broken, 12 kJ is released).
In order to emphasize the high energy "cost" of the phosphorus-oxygen bond in ATP, it is customary to denote it with the sign ~ and call it a macroenergetic bond. When one molecule of phosphoric acid is cleaved off, ATP is converted to ADP (adenosine diphosphoric acid), and if two molecules of phosphoric acid are cleaved off, then ATP is converted to AMP (adenosine monophosphoric acid). The cleavage of the third phosphate is accompanied by the release of only 13.8 kJ, so that there are only two macroergic bonds in the ATP molecule.
2. Formation of ATP in the cell
The supply of ATP in the cell is small. For example, in a muscle, ATP reserves are enough for 20–30 contractions. But a muscle can work for hours and produce thousands of contractions. Therefore, along with the breakdown of ATP to ADP, reverse synthesis must continuously occur in the cell. There are several pathways for the synthesis of ATP in cells. Let's get to know them.
1. anaerobic phosphorylation. Phosphorylation is the process of ATP synthesis from ADP and low molecular weight phosphate (Pn). In this case, we are talking about oxygen-free processes of oxidation of organic substances (for example, glycolysis is the process of oxygen-free oxidation of glucose to pyruvic acid). Approximately 40% of the energy released during these processes (about 200 kJ / mol of glucose) is spent on ATP synthesis, and the rest is dissipated in the form of heat:
C 6 H 12 O 6 + 2ADP + 2Fn -–> 2C 3 H 4 O 3 + 2ATP + 4H.
2. Oxidative phosphorylation- this is the process of ATP synthesis due to the energy of oxidation of organic substances with oxygen. This process was discovered in the early 1930s. 20th century V.A. Engelhardt. Oxygen processes of oxidation of organic substances proceed in mitochondria. Approximately 55% of the energy released during this (about 2600 kJ / mol of glucose) is converted into energy chemical bonds ATP, and 45% is dissipated as heat.
Oxidative phosphorylation is much more efficient than anaerobic syntheses: if only 2 ATP molecules are synthesized during glycolysis during the breakdown of a glucose molecule, then 36 ATP molecules are formed during oxidative phosphorylation.
3. Photophosphorylation- the process of ATP synthesis due to energy sunlight. This pathway of ATP synthesis is characteristic only for cells capable of photosynthesis (green plants, cyanobacteria). The energy of sunlight quanta is used by photosynthetics in the light phase of photosynthesis for the synthesis of ATP.
3. Biological significance of ATP
ATP is at the center of metabolic processes in the cell, being the link between the reactions of biological synthesis and decay. The role of ATP in the cell can be compared with the role of a battery, since during the hydrolysis of ATP, the energy necessary for various life processes ("discharge") is released, and in the process of phosphorylation ("charging"), ATP again accumulates energy in itself.
Due to the energy released during ATP hydrolysis, almost all vital processes in the cell and body occur: transmission of nerve impulses, biosynthesis of substances, muscle contractions, transport of substances, etc.
III. Consolidation of knowledge
Solving biological problems
Task 1. When running fast, we often breathe, there is increased sweating. Explain these phenomena.
Task 2. Why do freezing people start to stomp and jump in the cold?
Task 3. In the well-known work by I. Ilf and E. Petrov "The Twelve Chairs" among many useful tips you can also find this: "Breathe deeply, you are excited." Try to justify this advice from the point of view of the energy processes occurring in the body.
IV. Homework
Start preparing for the test and test (dictate test questions - see lesson 21).
Lesson 20
Equipment: tables on general biology.
I. Generalization of the knowledge of the section
Work of students with questions (individually) with subsequent verification and discussion
1. Give examples of organic compounds that include carbon, sulfur, phosphorus, nitrogen, iron, manganese.
2. How can a living cell be distinguished from a dead one by ionic composition?
3. What substances are in the cell in an undissolved form? What organs and tissues do they include?
4. Give examples of macronutrients included in the active centers of enzymes.
5. What hormones contain trace elements?
6. What is the role of halogens in the human body?
7. How are proteins different from artificial polymers?
8. What is the difference between peptides and proteins?
9. What is the name of the protein that is part of hemoglobin? How many subunits does it consist of?
10. What is ribonuclease? How many amino acids are in it? When was it artificially synthesized?
11. Why is the rate of chemical reactions without enzymes low?
12. What substances are transported by proteins through the cell membrane?
13. How do antibodies differ from antigens? Do vaccines contain antibodies?
14. What substances break down proteins in the body? How much energy is released in this case? Where and how is ammonia neutralized?
15. Give an example of peptide hormones: how do they participate in the regulation of cellular metabolism?
16. What is the structure of sugar with which we drink tea? What other three synonyms for this substance do you know?
17. Why is fat in milk not collected on the surface, but is in suspension?
18. What is the mass of DNA in the nucleus of somatic and germ cells?
19. How much ATP is used by a person per day?
20. What proteins do people make clothes from?
Primary structure of pancreatic ribonuclease (124 amino acids)
II. Homework.
Continue preparation for the test and test in the section "Chemical organization of life."
Lesson 21
I. Conducting an oral test on questions
1. Elementary composition of the cell.
2. Characteristics of organogenic elements.
3. The structure of the water molecule. The hydrogen bond and its significance in the "chemistry" of life.
4. Properties and biological functions of water.
5. Hydrophilic and hydrophobic substances.
6. Cations and their biological significance.
7. Anions and their biological significance.
8. Polymers. biological polymers. Differences between periodic and non-periodic polymers.
9. Properties of lipids, their biological functions.
10. Groups of carbohydrates distinguished by structural features.
11. Biological functions of carbohydrates.
12. Elementary composition of proteins. Amino acids. The formation of peptides.
13. Primary, secondary, tertiary and quaternary structures of proteins.
14. Biological function of proteins.
15. Differences between enzymes and non-biological catalysts.
16. The structure of enzymes. Coenzymes.
17. The mechanism of action of enzymes.
18. Nucleic acids. Nucleotides and their structure. The formation of polynucleotides.
19. Rules of E.Chargaff. The principle of complementarity.
20. Formation of a double-stranded DNA molecule and its spiralization.
21. Classes of cellular RNA and their functions.
22. Differences between DNA and RNA.
23. DNA replication. Transcription.
24. Structure and biological role of ATP.
25. The formation of ATP in the cell.
II. Homework
Continue preparation for the test in the section "Chemical organization of life."
Lesson 22
I. Conducting a written test
Option 1
1. There are three types of amino acids - A, B, C. How many variants of polypeptide chains consisting of five amino acids can be built. Specify these options. Will these polypeptides have the same properties? Why?
2. All living things mainly consist of carbon compounds, and silicon, the analogue of carbon, the content of which in the earth's crust is 300 times more than carbon, is found only in very few organisms. Explain this fact in terms of the structure and properties of the atoms of these elements.
3. ATP molecules labeled with radioactive 32P at the last, third residue of phosphoric acid were introduced into one cell, and ATP molecules labeled with 32P at the first residue closest to ribose were introduced into another cell. After 5 minutes, the content of inorganic phosphate ion labeled with 32P was measured in both cells. Where will it be significantly higher?
4. Studies have shown that 34% of the total number of nucleotides of this mRNA is guanine, 18% is uracil, 28% is cytosine, and 20% is adenine. Determine the percentage composition of the nitrogenous bases of double-stranded DNA, of which the specified mRNA is a mold.
Option 2
1. Fats are the "first reserve" in energy exchange and are used when the reserve of carbohydrates is depleted. However, in skeletal muscles, in the presence of glucose and fatty acids, the latter are used to a greater extent. Proteins as a source of energy are always used only as a last resort, when the body is starving. Explain these facts.
2. Ions of heavy metals (mercury, lead, etc.) and arsenic are easily bound by sulfide groups of proteins. Knowing the properties of the sulfides of these metals, explain what happens to the protein when combined with these metals. Why are heavy metals poisonous to the body?
3. In the oxidation reaction of substance A into substance B, 60 kJ of energy is released. How many ATP molecules can be maximally synthesized in this reaction? How will the rest of the energy be used?
4. Studies have shown that 27% of the total number of nucleotides of this mRNA is guanine, 15% is uracil, 18% is cytosine, and 40% is adenine. Determine the percentage composition of the nitrogenous bases of double-stranded DNA, of which the specified mRNA is a mold.
To be continued