Section 2. Nucleic acids.Lesson (6) 1. Structural organization of DNA:The chemical structure and spatial organization of

DNA and RNA, stabilizing interactions in structures. Heterocomplexes with DNA.

DNA polymorphism.Extraterrestrial, transposable DNA.

Question 1. The chemical structure and spatial organization of DNA and RNA, stabilizing interactions in structures.

Nucleic acids (NA) are heteropolymers, the monomers of which are nucleotides.

NA are contained in all living organisms, without exception, and are not only the custodian and source of genetic information, but also perform a number of other vital functions.

vital functions of nucleic acids

DNA RNA

Enzymatic – ribozymesTransport – tRNASignal – snRNASelf-copying – RNA polymeraseProtein-synthesizing – mRNA, rRNAStructural – rRNAInformation

TranslationDNA → protein

Interpherention DNA reparation

Information transfer

Horisontal Vertical

Intraspecific Interspecies Mather↔fetus Cell↔Cell

viruses?

Autocopiing – DNA-polimerasesStructural – telomeres

Information

Vertical information transfer

DNA↔protein SpermatozoidsEggs

Phenotype

Individual

Exa

ctIn

accu

rate

VariabilityPhenotypicIntraspecificSpeciation

Stability of the speciesConservative sites of DNA

Nucleic acids contain two types of nitrogenous bases: purine (purine) – adenine (A), adenine (G) derivatives and pyrimidine (purine) derivatives – adenine (C), uracil (U) and thymine (T).

adenine

purine

adenine

purine

adenine uracil thymine (Methyluracil)

The nucleotide consists of a nitrogenous base, a five-carbon sugar bound to it, and an orthophosphoric acid residue (Р).

Nucleic baseAdenine

The nucleoside part of the nucleotide –without a residue of phosphoric acid

Nucleotide

Ribose

Residue of phosphoricacid

Adenosine triphosphate Mg saltEach nucleotide is named after its nitrogenousbase, for example, adenylacid (or adenosine monophosphate –AMP):

adenine – ribose – R.AMP can be phosphorylated withadenosine diphosphate formation- ADP (adenine-ribose-P-P);phosphorylation of the latterleads to educationadenosine triphosphate (ATP).

In the cell, ATP exists only in the form of a magnesium salt –complexone.Each ATP molecule transfers Mg2+ to the active center of DNA and RNA polymerases.Without Mg2+ in the active center catalysis is impossible.

Joule is a work done when moving the point of application of force equal to one newton, at a distance of one meter in the direction of the force.

Calorie is the amount of heat required to heat 1 gram of water per 1 degree Celsius with a standard atmospheric pressure of 101 325 Pa.

1 cal = 4,1868 J exactly

1 J = 1 N·m=1 kg·m²/с²

In electricity, joule means the work done by the electric field forces in 1 second at a voltage of 1 volt to maintain a current strength of 1 ampere

Newton is a force that changes in 1 second the velocity of a body with a mass of 1 kg per 1 m / s in the direction of the force. In this way, 1 N = 1 kg·m/с2.

ATP is the universal energy accumulator in the cell.

The addition of a phosphoric acid residue to ADP using the energy of oxidation (during breathing) or light (for photosynthesis) represents "charging". Cleavage of phosphate from ATP with the formation of ADP is accompanied by the release of energy – "discharge".

Hydrolytic cleavage of the phosphoric acid residue from ATP liberates 12.6 kJ, hydrolysis of the second or third phosphate bond in ATP gives about 33.6 kJ.

The energy of the high-energy binding of ATP is consumed in the cell for various types of work. In addition to ATP, the macroergic compounds are other triphosphate nucleotides (GTP, CTF, UTP, TTF), which release a large amount of energy during hydrolysis of the terminal phosphate bond.

Using the previous slide, calculate the work that can be done when hydrolyzing one phosphate bond – be surprised.

In the formation of Nucleotide nucleotides are connected to each other with the help of a phosphorus-ether bond arising between a

phosphoric acid residue in the fifth ribose atom or deoxyribose and the hydroxyl of the third sugar atom. The resulting

polynucleotidethe chain has two ends:5 ', where the unbound

phosphate group, and3 ', which has a free

OH group withthe third atom

pentoses.

RNA nucleotides consisting of phosphoric acid, ribose and a nitrogenous base are connected by a 3 ', 5' phosphodiester bond,

this gives the polarity of the polynucleotide chain of the RNA molecule.

The pentose-phosphate backbone retains nitrogenous bases.

FUNCIES OF 2'-HYDROXIDE2'-hydroxyl does:1) it is impossible to fold a double-stranded RNA into a B-helix, but it allows it to form complex three-dimensional structures that are not available for DNA;

2) RNA is unstable, easily mutable and rapidly degradable.

The lack of 2'-hydroxyl in deoxyribose makes the DNA more structurally compliant and therefore more resistant to modification and damage, which is potentially useful for a carrier of genetic information. That's why DNA, but not RNA, can survive in nature for centuries.

Linear Ring Linear Ring Linear Ring Linear Ring

NUCLEIC ACIDS

DNA

Double-chine Single-chine Double-chine

RNA

Single-chine

Nomenclature of nucleotides forming DNA and RNA

Nitrogen base Nucleoside Nucleotide Three-letter notation

One-letter notation

Adenine Adenosine Adenosine monophosphate AMP АGuanine Guanosine Guanosine monophosphate GMP GCytosine Cytidine Cytidine monophosphate CMP С

Uracil Uridine Uridine monophosphate UMP UThymine Thymidine Thymidine monophosphate TMP Т

RNA types Size in nucleotidesgRNA – genomic RNA 10000-100000mRNA – information (matrix) RNA

100-100000

tRNA – transport RNA 70-90rRNA – ribosomal RNA several discrete classes from

100 to 500000sRNA – small RNA 100-300 several familiesRibozymes 200

Viral RNA

Family of small RNA

Antisense RNA (aRNA) – Closes a portion of the target mRNA from transcription.MicroRNA (miRNA) – stop the transcription of some genes (22 nucleotides).Small nuclear RNA, myRNA (snRNA) – splicing, support for the integrity of telomeres.Small nucleolar RNA (snoRNA) – short with two unpaired bases at the ends – splicing tRNA, mRNA, snRNA.Short RNA (shRNA) – form hairpins, turn off the expression of genes.Double-stranded RNAs (siRNA) are involved in antiviral responses (21 nucleotides).Peavy RNA (piRNA) – it associated with a particular type of protein – piwi terminate expression when spermatogenesis (26-30 nucleotides).mtRNA – unusual type of RNA, which acts as a tRNA and mRNA were detected in many bacteria and plastids. When stopping of the ribosome at the defective mRNA without a stop codon, Transfer-messenger RNA attaches a small peptide directing the protein to degradation.Guide (editor) RNA (gRNA) – edits DNA molecules and all types of RNA

RNA molecules have a secondary structure - hairpins, loops, spirals.

For the formation of a secondary structure, the presence of palindromic sequences is necessary.

tRNAs have a tertiary structure. ssRNA are rich in secondary and tertiary structures.

Tertiary structures are responsible for the catalytic properties of ribozymes (RNA + enzyme = Ribozyme).

Structural motifs of RNA

Pin

Nucleotide fusion

Pin fusion

Pulling out two pins

Branching

Y-branch

Pin with branch

Pseudo-node

Transport RNAs (tRNAs) are short molecules (70-90 nucleotides) with secondary and tertiary structures.Secondary structure is cloverleaf.The CCA sequence at the 3 'end is the same for all tRNAs.The amino acid is added to the terminal adenosine (A).

The presence of thymine (T), pseudouridine (Ψ) in the (TΨC-loop), and dihydrouridine (DSU) (in D-loop) in tRNA is minor, i.e. rarely found in RNA nucleotides, indicates the features of its the structures necessary for an error-free recognition by enzymes, to protect against the action of ribonucleases (therefore tRNA-long-lived, unlike mRNA).

Structure of transport RNA

The tertiary structure in the projection on the plane has the form of a boomerang.The variety of primary structures of tRNA - 61 + 1 - in the number of codons (corresponding to the number of anticodons in tRNA) + formyl-methionine tRNA, in which the anticodon is the same as for methionine tRNA.The variety of tertiary structures is 20 (by the number of amino acids).

Ribosomal rRNAs function as skeletons of ribosomal subunits and participate in the synthesis of polypeptides

23S rRNA enters the catalytic peptidyl transferase center16S rRNA is required for installation on the 30S subunit of the initiation codon mRNA5S rRNA - for the correct orientation of aminoacyl-tRNA on the ribosome.

All rRNAs have a developed secondary structure: about 70% of the nucleotides are assembled in hairpins.

S – Svedberg`s units is an off-system unit for measuring the sedimentation coefficient, which is defined as the ratio of the sedimentation rate of particles suspended in water to centrifugal acceleration in centrifuges and ultracentrifuges.

Small RNA

sRNA were detected in an amount of 103-105 copies per cell.They are enriched with uracil, therefore they are called U1, U2 ... Size from 100 to 300 nucleons.Encoded in the nucleus, but work both in the nucleus (small nuclear - SN), and in the cytoplasm (small cytoplasmic - SC). in the nucleus of snRNA are part of the RNP (ribonucleoprotein complexes) involved in polyadenylation and splicing in the cytoplasm are part of the informosome.A small RNA of U4 is present in the complexes involved in polyadenylation. If antibodies to proteins that bind to U4 are obtained, polyadenylation and splicing do not occur.

(In case of lupus erythematosus antibodies are produced to proteins of the complex with U4)

Structure of deoxyribonucleic acid

The skeleton of a single strand of DNA has a polarity.

The pentose-phosphate backbone retains nitrogenous bases.

Polynucleotide chains of the primary structure of DNA reach gigantic sizes, therefore they are formed with certain regularities.The rules of the Chargaffthe sum of purine nucleotides is equal to the sum of pyrimidine nucleotides, ie, A + T / T + A = 1the adenine content is equal to the content of thymine (A = T, or A / T = 1);the content of guanine is equal to the content of cytosine (G = C, or G / C = 1);the number of 6-amino groups is equal to the number of 6-keto groups of bases contained in DNA: G + T = A + C;only the sum of A + T and T + U is variable. If A + T> T-U, then this is the AT type of DNA; If F + U> A + T, then this is a GC type of DNA.These rules indicate that in the construction of DNA should be observed quite strict correspondence (pairing) of non-purine and pyrimidine bases in general, namely, thymine with adenine and cytosine with guanine.

The main functions of DNA

Reproduction and transfer of genetic information in generations of cells and organisms. This function is provided by the replication process.

DNA is the carrier of genetic information, which is ensured by the existence of a genetic code.

Realization of genetic information in the form of proteins, as well as any other compounds formed with the help of protein-enzymes. This function is provided by the processes of transcription and translation.

Forms of double-stranded DNADNA can form several types of double helixes. Now known A, B, C-E, H and Z-forms.

A molecule of high humidity DNA was called B-form. This is the dominant structural DNA type under physiological conditions (low salt concentration, high degree of hydration) - the main form of double-stranded DNA (the Watson-Crick model).The spiral of such a molecule is 3.4 nm.The turn has 10 complementary pairs of nitrogenous bases.The planes of the nitrogenous bases are perpendicular to the axis of the helix.Adjacent complementary pairs are rotated relative to each other by 36 °.The diameter of the helix is 20Å, the purine nucleotide occupies 12Å, and the pyrimidine nucleotide is 8Å.

Z-form of DNA - is formed in places of the B-form of DNA, where purines alternate with pyrimidines or in repeats containing methylated cytosine.

A DNA form of lower humidity was called the A-form (Rosalind Franklin model).The A-form is formed under conditions of less high hydration and with a higher content of Na+ or K+. This broader right-handed conformation has 11 pairs of nitrogenous bases per turn. The planes of the nitrogenous bases have a stronger inclination to the axis of the helix, they are deviated from the normal to the axis of the helix by 20 °. Hence, there is an internal emptiness of 5Å in diameter. The distance between adjacent nucleotides is 0.23 nm, the length of the loop is 2.5 nm, the diameter of the helix is 2.3 nm.The A-form has a RNA-DNA helix in the matrix-seed complex, as well as the RNA-RNA spiral and hairpin RNA structures (the 2'-hydroxyl ribose group does not allow the RNA molecules to form the B-form). A-form of DNA is found in spores. It has been established that the A-form of DNA is 10 times more resistant to the action of UV rays than the B-form.

A-form and B-form are called canonical forms of DNA.

Forms C-E are also right-handed, their formation can be observed only in special experiments, and, apparently, they do not exist in vivo. The C-form of DNA has a structure similar to B-DNA. The number of base pairs per turn is 9.33, the length of the helix is 3.1 nm. The base pairs are inclined at an angle of 8 degrees from the perpendicular position to the axis. In the C-form, natural and synthetic DNA polynucleotides can pass.C-form is the basis for the construction of triple-stranded DNA forms.I-motif, or I-form DNA, consists of two parallel C-strands intercalated according to the principle "from head to tail".H-form DNA and triple DNA helix - are formed in the presence in the same chain of the normal Watson-Cricova duplex area containing only purines, and in the second chain, respectively, complementary to them pyrimidines.G-quadruplex (G-4) is a four-stranded DNA helix, where 4 guanine bases from different chains form G-quartets (G-tetrads) bonded by hydrogen bonds to form G-quadruplexes.

The Holidean compound is the formation of a triple-stranded DNA with the participation of the C-form

See slide 27See slide 27

Triple helix DNA H-form

Triad T= A⋅T Triad C= G⋅CThe component blocks Py-Pu-Py of the triplex are the canonical isoform TAT and the CGC triad.

Hugsten's mating is shown between the bases of the red color,the Watson-Crick mating is between the base of the red and black color.

Triple Helix Py-Pu-PyThe purine chain forms the canonical double helix with the pyrimidine. The third purine chain lies in the largegroove of this double helix (marked white). In the caption to the figure, the Watson-Crick interaction is markedby a line, Hugsten's interaction is marked with an asterisk, plus the protonation sites for stabilizing the complexare noted.

The solid black line shows theWatson-Crick pairs, the interruptedHugsten's interaction in the largegroove of duplex DNA in theformation of a triplex

The formationof a triple helixOne of thefilaments (darkblue) remainsunstructured

Orientation of the DNA helixSchematic representation of DNAtriple helix, antiparallel and parallelorientation

G-quadruplex is a 4-chain form of DNA deposition in telomeres.Telomeres of all vertebrates consist of numerous repetitions of six nucleotides of TTAGGG, telomeres of all insects from TTAGG repeats, and TTTAGGG into most of the plant telomers.

Very similarity, yes ?? TTAGGG - we TTAGG - insects TTTAGGG - plants

The Z-form of DNA is a left-handed spiral formed during the neutralization of the negative charge on the phosphodiester backbone, this is observed in DNA sections where the purines alternate with pyrimidines (for example, 5'-GCGCGC-3 '), or in the repeats 5'-CGCGCG-3' , containing methylated cytosine. In this case, other parts of DNA in the chain remain in the classical B-form.Z-DNA is the least twisted (12 base pairs per turn) and the thinnest known in nature.The distance between adjacent nucleotides is 0.38 nm, the length of the loop is 4.56 nm, and the Z-DNA diameter is 1.8 nm.In addition, the appearance of this DNA molecule is distinguished by the presence of one groove. The Z-form of DNA was found in the cells of prokaryotes and eukaryotes.

Transition of the B-form to Z-DNA. B-DNA is rewound by negative super-consistency (rotation of the two ends in different directions), which squeezes out two inverted base pairs (two B-Z junctions). Further unwinding forms the left Z-DNA between two sections of DNA, spinning in opposite directions.

Tertiary structure of DNA

Tertiary structure of DNA is formed as a result of additional twisting in the space of a double-helix molecule -its supercoiling. The supercoiling of the DNA molecule in eukaryotic cells is carried out in the form of complexes with histone and non-histone proteins.

Histone proteins chromatinHistones are simple proteins that make up to 50% chromatin. In all studied cells of animals and plants, five main classes of histones were found:H1, H2A, H2B, H3, H4,different in size, amino acid composition and charge (always positive).

Histone H1, is not a unique molecule, and a class of proteins consisting of several closely related proteins with overlapping amino acid sequences, their common property is the enrichment with lysine.

Histones H3 and H4 are referred to arginine-rich, because of the relatively high content of this amino acid in them. These histones are the most conserved of all the proteins studied: their amino acid sequences are almost the same even in remote species such as a cow and peas (only two amino acid substitutions).

Histones H2A and H2B are a moderately enriched lysine protein. Various objects within these histone groups exhibit interspecific variations in their primary structure, in the sequence of amino acids.

The mammalian histone Н1 consists of a single polypeptide chain containing approximately 215 amino acids. The dimensions of the other histones range from 100 to 135 amino acids. They are all helical and twisted into a globule with a diameter of about 2.5 nm, contain an unusually large amount of positively charged amino acids of lysine and arginine.Histones can be acetylated, methylated, phosphorylated, poly (ADP) -ribosylated, and histones H2A and H2B-covalently bound to ubiquitin. It is assumed that this is their ability to interact with DNA and provide one of the mechanisms for regulating the action of genes.Histones interact with DNA mainly through ionic bonds (salt bridges) formed between negatively charged phosphate groups of DNA and positively charged lysine and arginine histone residues.

Non-histone proteins of chromatinIsolated up to 590 different fractions of DNA-binding non-histone proteins. They are also called acidic proteins, since their structure is dominated by acidic amino acids (they are polyanions).A variety of non-histone proteins is associated with specific regulation of chromatin activity. For example, enzymes required for DNA replication and expression can temporarily bind to chromatin.Other proteins, for example, participating in various regulatory processes, bind to DNA only in specific tissues or at certain stages of differentiation. Each such protein is complementary to a certain sequence of DNA nucleotides (DNA site).

To this group of proteins include: a family of site-specific proteins such as "zinc fingers." Each "zinc

finger" recognizes a certain site consisting of 5 nucleotide pairs. a family of site-specific proteins - homodimers. A fragment of such

protein, contacting with DNA, has a "spiral-rotate-helix" structure. high mobility proteins (HMG proteins) are a group of structural and

regulatory proteins that are constantly associated with chromatin. They are characterized by a high content of charged amino acids. Due to their low molecular weight, HMG proteins have a high mobility with electrophoresis in a polyacrylamide gel.

enzymes of replication, transcription and repair.

With the participation of structural, regulatory proteins and enzymes involved in the synthesis of DNA and RNA, the nucleosome strand is transformed into a highly condensed complex of proteins and DNA. The structure is 10,000 times shorter than the original DNA molecule.

Structural organization of DNA (chromosomes levels of compactification)

Plot of double helix DNA

Nucleosomal levelDNA is wound on protein "beads" - proteins -histones with the formation of a nucleosomalfilamentSolenoid levelTwisting the nucleosome strand to form a chromatin fiber - fibrils. Compact stacking of "beads" like a solenoid or superbide

Loop levelPacking of chromatin fibrils with loops. The loops are fixed with a special bobbin matrix (scaffold)

Domain levelFormation of looping domains, which, with their base, attach to the protein matrix in the SAR (scaffolds attachment regions) regions - fragments of DNA with a high content of A / T pairs of nucleotides

Chromosome levelThe last (highest) level of DNA compactification. Mitotic chromosome consisting of two chromatids

scaffold chromosome

scaffold chromosome

Question 2. Polymorphism of DNA.DNA polymorphism - existence in one speciesdifferences in the nucleotide sequence.The source of DNA polymorphism is mutations,which can not only be transmitted by a descendant, but alsomultiply in the population.When one of the variants of nucleotide sequencesof a particular region of DNA is detected more thanin 1% of individuals, this variability is most oftencalled DNA polymorphism, if less than 1%just a mutation.The difference between mutations and polymorphism is sufficientconditionally.

The causes of the appearance of mutations are external: • Cosmic and solar radiation (UV, X-ray radiation); terrestrial radiation. • Mutagenes of the environment (mainly anthropogenic nature: industrial and domestic waste, nuclear explosions, fertilizers and pesticides, food mutagens, drugs).

Nitrosamines - are formed from tobacco alkaloids (malignant tumors of the lungs, esophagus ...).In fried meat → heterocyclic amines, in smoked → polycyclic hydrocarbons

and also acetaldehyde, acrolein, and

polonium

The reasons for the occurrence of mutations are internal:

Infections - viral. Breeding in cages host, viral particles build "master" genes into your DNA.

Errors in DNA replication (not enough effective work of repair systems). Everytime, when the cell is divided, copied> 3 billion. nucleotides!

The phenomenon of exact doubling of the DNA molecule, at the basis The complementarity of the bases of this molecule, is the molecular basis heredity and provides the future of the whole species.

The more times DNA is copied (replicated), the moremore errors accumulate in it.Replication errors are the reason that a newborn person,"Male" mutations are on average 5 times more than "female" mutations.

Oocyte - before meiosis passes through 25 mitoses.

The number of mitoses through which spermatogonia passes throughmeiosis, depends on the age of the man:if 18 years - 100 mitosesif 50 years - 800 mitoses

RESULT:From the mother, the child receives an average of 15 mutations, regardless of herage.From father - depending on age:father 20 years - 25 mutations,father 40 years old - 65,father 50 years - 85 mutations.

Mutations continue after conception!Only in the brain at the time of birth, up to 400 mutations are observed.

Types of genetic polymorphism:polymorphism of single nucleotides -SNP (Single Nucleotide Polymorphisms) is the most common type variability of nucleotide DNA sequences (99% of allchanged options).We differ from each other in 1 positions of nucleotides from 800 to 1000.SNP is the main cause of individual genetic differences.

Short tandem repeats - STR(Short Tandem Repeat) - the difference innumber of short nucleotide sequences (mini

(> 7) and microsatellites (1-7)).

STR cause some hereditary diseases only in humans.

SNP are responsible for the presence of qualitatively new properties of the body, the frequency of their distribution differs between different ethnic or geographical groups, in accordance with certain conditions of vital activity of a specific population.

In some cases, SNP can lead to amino acid substitutions with the development of a monogenic disease.

So, in many countries in Asia and Africa, where adults do not drink milk, lactase is no longer synthesized after the age of five. In this case, the use of cow's milk leads to a digestive disorder.

In some Europeans, this enzyme is synthesized due tothe presence of a mutation in the regulatory region of the encoding LCT gene, namely: C-13910T, G-22018C, etc., which appeared about 9-10 thousand years ago after the appearance of dairy cattle breeding.

The payment for improving survival and fitness heterozygous carriers of mutations may be fatal homozygous carriers, which occur an order of magnitude less frequently.

For example, in the heterozygous state, the mutation of the HEXA genecauses immunity to mycobacteria tuberculosis, in homozygous - hereditary disease of Thea-Saks.

Carriers of sickle-cell anemia mutation do not get sick malaria.

Mutations of the CFTR gene (namely, ΔF508, G542X, R553X, W1282X, N1303K, dele2,3 (21kb), etc.), which lead to a disturbance in the regulation of the water-electrolyte balance, cause cystic fibrosis in the homozygous state, and in the heterozygous state reduce the intensity discharge of fluid through the walls of the intestine.

The HEXA gene, the hexosaminidase A gene, is localized on the 15th human chromosome at position q23-q24 (Takeda K., 1990; Nakai H., 1991).

The HBB gene - its mutation leads to the replacement of glutamic acid in the sixth position of the β-chain of hemoglobin with valine, resulting in the synthesis of abnormal hemoglobin S, which under polymerization conditions forms long cords, resulting in erythrocytes becoming crescent-shaped. In the heterozygous state it provides resistance to malaria.

CFTR gene Cystic Fibrosis Transmembrane conductase Regulator - the gene of the transmembrane regulatory protein, the mutation of which causes cystic fibrosis, is located on the 7th chromosome at the locus q31.2.

If the mutation does not pose a threat to the existence of the species, or even is useful, then for some time it spreads among the population. This leads to the fact that about 90% of the comparative nucleotide sequences of different people will differ on separate bases, which is called polymorphism of simple nucleotides.

Varies between taxa:

In yeast, it reaches 20%.In mammals, up to 60%Plants can exceed 80%.

Size of STR regions in genomes

DNA repeats

Frequent repetitions

Middle repetitions

Satellite DNA

with long end repetitions

without long end repeats

with short dispersed repeats

Intermittent retrotransposons

Tandem repetitions

Multiple copies of genes

Mini satellites

Micro satellites

Dinucleotidesvariable number of

tandem repeatsrRNAgenes

Classification of STR1. By mutual orientationstraight,inverted,symmetrical repetitions,palindromes,complementary palindromes

Madam I`m Adam – text symmetry.Palindromes (shifters) - the same alternation of nucleotides along the chain from right to left and from left to right ("hut"). The palindrome is characterized by the presence of inverted repeats of base sequences having second-order symmetry with respect to two DNA strands.

Such sequences are self-complementary and tend to form hairpin or cruciform structures. Hairpins help regulatory proteins to recognize the place of reading the genetic text of chromosome DNA.

If the inverted repetition is present in the same chain, DNA such a sequence is called mirror repetition.Mirror repetitions do not have self-complementary properties and, therefore, are not capable of forming hairpin or cruciform structures.The presence of self-complementary sequences in the composition of RNA or single-stranded DNA serves as the main reason for folding in solutionsnucleic chain into a certain spatial structure, differing in the formation of a set of "pins".

Palindromes – specific sequences in double-stranded DNA possessing second-ordersymmetry. This means that when the double-stranded sequence is rotated 180 °relative to the axis perpendicular to the plane in which the bases are located, theirpositions in the two strands of DNA will not change.To overlap one repetition with another one, it is necessary first to rotate 180 ° relativeto the horizontal axis, and then 180° relative to the vertical axis (as shown by thecolored arrows.

Mirror repeats are specific sequences that differ in symmetry in each DNA strand.To superimpose one repetition on the other, one single rotation of the sequence at180 ° around the vertical axis is sufficient (Nelson D.L., Cox M.M., LehningerPrinciples of Biochemistry, W. H. Freeman (ed.) San Francisco, 2004).

Шпилечная структура РНКПалиндромная последовательностьв РНК, способная формироватьальтернативную структуру за счетвнутрицепочечного спариванияоснований. Шпилька, характернаядля одноцепочечной РНК.Крестообразная структура ДНКПалиндромная последовательностьв ДНК, формирующая альтернатив-ную структуру за счет внутрицепо-чечного спаривания оснований.Двойной участок ДНК, содержащийпалиндром, образующий крестооб-разную структуру.

2. Based on renaturationFast repetitionsModerate repetitionsUnique genes

Repeats classification

Satellite DNADNA with tandem-organized high repetitive sequencesIn some species, these repeats constitute the majority of genomic DNA. For example, in a kangaroo rat (Dipodomys ordii), more than 50% of the entire genome consists of three repeated sequences: AAG (2.4 billion copies), TTAGGG (2.2 billion copies) and ACAAGCGGG (1.2 billion copies)

Satellite classification

1. Microsatellites - from 1 to 10 base pairs in the main repeating block

2. Minisatellites - with a large number of base pairs in individual repetition

Satellite types

1. Classical satellites

The satellite 1, having an elementary repeating unit of 42 n. p., and found on chromosomes 3, 4, 13, 14, 15, 21, 22;The satellite 2, having an elementary repeating unit of length 5 n. p., and found on chromosomes 1, 2, 10, 16;The satellite 3, having an elementary repeating unit of length 5 n. p., and found on the chromosomes 1, 5, 9, 10, 13, 14, 15, 17, 20, 21, 22, Y;

n. p. – nucleotide pare

Satellite types

2. α-satellite repeats having an elementary repeating unit of length 171 n. p. and found on all human chromosomes;

3. β-satellite repeats having an elementary repeating unit of length 68 n. p., and found on the chromosomes 1, 3, 9, 13, 14, 15, 21, 22, Y;

4. γ-satellite repeats having an elementary repeating unit of length 220 n. p., and found on chromosomes 8, X

5. satellite repeats having an elementary repeating unit of length 48 n. p., and found on the chromosomes 13, 14, 15, 21, 22, Y;

6. Sn5-satellite repeats, found on chromosomes 2, 13, 14, 15, 20, 21, 22 (the length of the repeating unit is unknown).

Features of satellites1. This DNA is never translated and occurs in constitutive heterochromatinIn the chromosome, heterochromatin and euchromatin regions alternate.Areas of chromosomes that, depending on the stages of the cell cycle, can be in a state of both hetero- and euchromatin is called facultative heterochromatin.Areas that are always densified are constitutive heterochromatin. As a rule, there are no genes in it.2. Satellite DNA is necessarily located in the centromeric region at the locations of satellite DNA is maximally compacted. In constitutive heterochromatin, all four levels of DNA packaging are present even in the interphase.3. The satellite DNA is always located in tandem for 100-200 units in the block.4. The satellite DNA that has recently formed in one territory has different satellite DNA.

2. Mild repeats. Transcribed and transmitted or only transcribed DNA sequences

Genes Regulatory plotsTranscribed and broadcasted

Genes of ribosome proteins, histone genes, membrane protein genes, cytoskeletal proteins, immunoglobulin genes

Transcribed

The genes of rRNA, sRNA, tRNA

Enhanced modules, ori,Replication, promoters and terminators of transcription

I. Genes classification(including unique genes)

1. Unique genes that have a specialized function.For example, globin, insulin and other genes. They are expressed only in certain cells.

2. Unique genes possessing common functions, expressed in the overwhelming majority of cells.These genes are poorly understood.

3. Multiple grouped genes.These are the rRNA genes, part of the tRNA genes, part of the histone genes.

4. Multiple scattered genes.This is the rest of the histone genes, the remaining tRNA genes and most sRNA genes, as well as MDG (mobile dispersed (scattered) genes).

II. Genes classification

1. genes of "housekeeping" (encode what is always needed for any cell regardless of the type of tissue: histone genes, tRNA genes, rRNA, etc.)

2. genes of "luxury" (these are genes that are expressed in the cells of certain tissues and at certain times).

Structure of the human genome1. 63-74% of the length of the genome is

occupied by intergenic spaces, and half of them are repetitions.

2. The human gene inside is "empty": 95% of intragenic DNA is introns.

3. The total length of the protein of the coding DNA is about 1% of human genomic DNA.

4. The length encoding human DNA is only 3 times the length of the bacterial genome.

Question 3. Extraterrestrial, transposable, viral DNA.

Extracerebral (extrachromosomal) DNA prokaryotes and eukaryotes:1. DNA of plasmids (bacteria, lower fungi, etc.).2. DNA of organelles (mitochondria, chloroplasts, kinetoplasty).3. DNA of amplified and transposable genes

Integrative plasmids(episomes) Transmissive plasmids

mobilizing plasmids(conjugative) R- plasmids

Col- plasmids

Ent- plasmidsF- plasmids

Hly- plasmids

Plasmids

mobilizable plasmids(non-conjugative)

Plasmids is extrachromosomal mobile genetic structures, which are closed rings of double-stranded DNA, their distinctive ability is autonomous copying (replication).Episomes can be integrated (integrated) into the chromosome and replicated with it.The transmissible (conjugative) plasmids can be transferred from one bacterium to another.Non-transmissive plasmids can not be transferred from one bacterium to another.R-plasmids carry genes responsible for multiple resistance to drugs -antibiotics, sulfonamides, etc.F-plasmids - the sexual factor of bacteria, which determines their ability to conjugate and form sexual pylae through which the transfer of the main DNA molecule or transmissible plasmids occurs.Ent-plasmids, determine the production of enterotoxin.Col-plasmids are colicins.Hly-plasmids - hemolysins.

Plasmids that control the destruction of many organic compounds and other properties are known. Due to the transfer factor, these plasmids are conjugative.

Mobilizable (non-conjugative) plasmids do not contain determinants that confer on bacterial cells the properties of genetic donors, and therefore they are not capable of self-transfer from one cell to another.Mobilizing (conjugative) plasmids transfer the mobilizable plasmids to the recipient cells.

Plasmids can determine the virulence of bacteria, for example plague pathogens, tetanus, the ability of soil bacteria to use unusual sources of carbon, control the synthesis of protein antibiotic-like substances -bacteriocins, plasmid-determined bacteriocinogenia, etc.The existence of a multitude of other plasmids in microorganisms suggests that similar structures are widespread in a wide variety of microorganisms.

Plasmids are susceptible to recombinations, mutations, can be eliminated (removed) from bacteria, which does not affect their basic properties. Due to the rapid self-copying and the possibility of conjugation transfer of plasmids within the species, between species or even genera, plasmids play an important role in the evolution of bacteria.

Mitochondrial DNA is characterized by small dimensions.For example, the size of DNA molecules of mitochondria of different animals (including flatworms, insects and mammals) is 15 700 - 20 000, human - 16 569 bp.In Trypanos and Paramecia, it is 22,000 and 40,000 bp; chloroplasts 12,000 - 200,000 bp, in yeast - 78,000 bp.In many cases it has been shown that the DNA of mitochondria and chloroplasts consist entirely of nucleotide sequences homologous to sequences of chromosomal DNA.

The human mitochondrial genome consists of 37 genes that encode native ribosomal RNAs (12S- and 168-rRNAs) and 22 different transport RNAs, as well as different polypeptides, including subunit components of cytochrome C cytochrome C, subunits of ATPase, cytochrome B and nine other proteins whose functions are not known.The genome of chloroplasts of a number of higher plants consists of 120 genes. They encode 4 ribosomal RNAs, 30 ribosomal proteins, part of the subunits of the chloroplast RNA polymerase, part of the proteins contained in photosystems I and II, the protein subunits of ATP synthetase and individual enzymes of the electron transport chain, as well as the protein subunit of ribulose-bisphosphate carboxylase and very many tRNAs. The chloroplastic genome is very similar to the bacterial genome, both in organization and in function.

In the mitochondrial genome of humans, probably introns, but introns are found in the DNA of the chloroplasts of some higher plants, as well as in the DNA of mitochondria of fungi. It is believed that the chloroplast genomes of higher plants remain unchanged for about several million years. It is possible that such an antiquity is also characteristic of the mitochondrial genomes of mammals, including humans.DNA, which is part of kinetoplastics, consists of thousands of ring double-stranded molecules measuring 20-38 (maxi-rings) or 0.5-2.5 (mini-rings) thousand items; maxi-rings are identical to mitochondrial DNA of eukaryotes, while the biological role of mini-rings is still unclear;Ring DNA is characteristic for trypanosomes of the order Kinetoplastida.

DNA amplified genesThis DNA is found in the form of extrachromosomal ring molecules. For example, when eukaryotic cells are cultured in media containing drugs, selection of resistant cells with an increased number of copies of the resistance control gene takes place. Cells of many tumors also contain extrachromosomal amplified genes. These molecules are found in the cytosol, in the nucleus and mitochondria of the cells of many eukaryotic organisms.Almost half of the human genome consists of various transposable elements (transposable elements, TEs). They fall into two main classes: DNA transposons (DNA transposones) and retroelements (retroelements).

DNA transposons change the evolutionary trajectory of their host due to the following mechanisms:1) through a change in the function of genes by inserting genes, regulatory elements, "shuffling" exons and introns;2) through the induction of chromosomal permutations;3) as sources of coding and non-coding DNA, which allows the emergence of various genetic novelties, such as new genes and regulatory sequences.Transposable elements of prokaryotic cells move along the route of chromosome plasmid another plasmid chromosome.Transposition of transposons is provided by a specialized replicative process, which is not associated with the generation of extrachromosomal forms.Under experimental conditions, any transposon can be incorporated into virtually any plasmid.

Genetic elements similar to transposable ones also exist in eukaryotic cells, where they are represented by different repeating DNA sequences. Some of these elements are transposed as a result of re-inclusion (reinsertion) into the genome of the product of reverse transcription (copies of RNA). Such elements are called retroelements (retrotransposons).On the contrary, other elements are transposed directly through copies of DNA.The most famous retroelements are retrotransposons with short terminal repeats. Such are the retrotransposons I or R2 in Drosophila, Line in mammals, ingi in trypanosomes.

Copies of these retrotransposons encode the proteins necessary for reverse transcription, i.e. their transposition is performed using RNA as an intermediate.To this category of retroelements also belong sequences with long terminal repeats, in particular the sequences of copia and gypsy Drosophila, the yeast TY-factor and LI-elements in mammals.In these sequences, repetitions reach 500 bp.Retrotransposons also consider many sequences that, in addition to insertion ability, have infectious properties, these are separate retroviruses: bird leukemia, mammalian leukemia, mammalian immunodeficiency.

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