Chapter 2. Structure and functions of proteins Proteins are high-molecular nitrogen-containing organic compounds, consisting of amino acids connected into polypeptide chains using peptide bonds, and having a complex structural organization. History of the study of proteins In 1728

Functioning of Proteins Each individual protein, which has a unique primary structure and conformation, also has a unique function that distinguishes it from all other proteins. A set of individual proteins performs many diverse and complex tasks in a cell.

Post-translational changes in proteins Many proteins are synthesized in an inactive form (precursors) and, after convergence with ribosomes, undergo postsynthetic structural modifications. These conformational and structural changes in polypeptide chains received

Levels of study of metabolism Levels of study of metabolism:1. Whole organism.2. Isolated organs (perfused).3. Tissue sections.4. Cell cultures.5. Tissue homogenates.6. Isolated cellular organelles.7. Molecular level (purified enzymes, receptors and

Digestion of proteins in the gastrointestinal tract Digestion of proteins begins in the stomach under the action of enzymes in gastric juice. Up to 2.5 liters are secreted per day and it differs from other digestive juices in its highly acidic reaction, due to the presence

The breakdown of proteins in tissues is carried out using proteolytic lysosomal enzymes cathepsins. Based on the structure of the active center, cysteine, serine, carboxyl and metalloprotein cathepsins are distinguished. Role of cathepsins:1. creation of biologically active

The role of the liver in the metabolism of amino acids and proteins The liver plays a central role in the metabolism of proteins and other nitrogen-containing compounds. It performs the following functions: 1. synthesis of specific plasma proteins: - synthesized in the liver: 100% albumins, 75 – 90% β-globulins, 50%

Characteristics of blood serum proteins Proteins of the complement system - this system includes 20 proteins circulating in the blood in the form of inactive precursors. Their activation occurs under the influence of specific substances with proteolytic activity.

Proteins are organic substances. These high-molecular compounds are characterized by a certain composition and, upon hydrolysis, break down into amino acids. Protein molecules can come in many different forms, many of them consisting of several polypeptide chains. Information about the structure of a protein is encoded in DNA, and the process of synthesis of protein molecules is called translation.

Chemical composition of proteins

Average protein contains:

• 52% carbon;
• 7% hydrogen;
• 12% nitrogen;
• 21% oxygen;
• 3% sulfur.

Protein molecules are polymers. In order to understand their structure, it is necessary to know what their monomers - amino acids - are.

Amino acids

They are usually divided into two categories: constantly occurring and occasionally occurring. The first include 18 and 2 more amides: aspartic and glutamic acid. Sometimes there are only three acids found.

These acids can be classified in different ways: by the nature of the side chains or the charge of their radicals, they can also be divided by the number of CN and COOH groups.

Primary protein structure

The order of alternation of amino acids in a protein chain determines its subsequent levels of organization, properties and functions. The main one between monomers is peptide. It is formed by the abstraction of hydrogen from one amino acid and the OH group from another.

The first level of organization of a protein molecule is the sequence of amino acids in it, simply a chain that determines the structure of protein molecules. It consists of a “skeleton” that has a regular structure. This is the repeating sequence -NH-CH-CO-. Individual side chains are represented by amino acid radicals (R), their properties determine the composition of the protein structure.

Even if the structure of protein molecules is the same, they can differ in properties only because their monomers have a different sequence in the chain. The order of amino acids in a protein is determined by genes and dictates certain biological functions to the protein. The sequence of monomers in molecules responsible for the same function is often similar in different species. Such molecules are identical or similar in organization and perform the same functions in different types of organisms - homologous proteins. The structure, properties and functions of future molecules are established already at the stage of synthesis of a chain of amino acids.

Some common features

The structure of proteins has been studied for a long time, and analysis of their primary structure has made it possible to make some generalizations. A larger number of proteins are characterized by the presence of all twenty amino acids, of which there is especially a lot of glycine, alanine, glutamine and little tryptophan, arginine, methionine, and histidine. The only exceptions are some groups of proteins, for example, histones. They are needed for DNA packaging and contain a lot of histidine.

Any type of movement of organisms (muscle work, movement of protoplasm in a cell, flickering of cilia in protozoa, etc.) is carried out by proteins. The structure of proteins allows them to move, form fibers and rings.

The transport function is that many substances are transported across the cell membrane by special carrier proteins.

The hormonal role of these polymers is immediately clear: a number of hormones are proteins in structure, for example insulin, oxytocin.

The reserve function is determined by the fact that proteins are able to form deposits. For example, egg valgumin, milk casein, plant seed proteins - they store a large amount of nutrients.

All tendons, articular joints, skeletal bones, and hooves are formed by proteins, which brings us to their next function - support.

Protein molecules are receptors, carrying out selective recognition of certain substances. Glycoproteins and lectins are especially known for this role.

The most important factors of immunity are antibodies and are proteins in origin. For example, the blood clotting process is based on changes in the fibrinogen protein. The inner walls of the esophagus and stomach are lined with a protective layer of mucous proteins - lycins. Toxins are also proteins in origin. The basis of the skin that protects the body of animals is collagen. All of these protein functions are protective.

Well, the last function is regulatory. There are proteins that control the functioning of the genome. That is, they regulate transcription and translation.

No matter how important the role proteins play, the structure of proteins was unraveled by scientists quite a long time ago. And now they are discovering new ways to use this knowledge.

Protein biosynthesis.

1. The structure of one protein is determined:

1) a group of genes 2) one gene

3) one DNA molecule 4) the totality of genes of an organism

2. The gene encodes information about the sequence of monomers in the molecule:

1) tRNA 2) AA 3) glycogen 4) DNA

3. Triplets are called anticodons:

1) DNA 2) t-RNA 3) i-RNA 4) r-RNA

4. Plastic exchange consists mainly of reactions:

1) decomposition of organic substances 2) decomposition of inorganic substances

3) synthesis of organic substances 4) synthesis of inorganic substances

5. Protein synthesis in a prokaryotic cell occurs:

1) on ribosomes in the nucleus 2) on ribosomes in the cytoplasm 3) in the cell wall

4) on the outer surface of the cytoplasmic membrane

6. The broadcast process occurs:

1) in the cytoplasm 2) in the nucleus 3) in mitochondria

4) on the membranes of the rough endoplasmic reticulum

7. Synthesis occurs on the membranes of the granular endoplasmic reticulum:

1)ATP; 2) carbohydrates; 3) lipids; 4) proteins.

8. One triplet encodes:

1. one AK 2 one sign of an organism 3. several AKs

9. Protein synthesis is completed at the moment

1. recognition of a codon by an anticodon 2. appearance of a “punctuation mark” on the ribosome

3. entry of mRNA into the ribosome

10. The process that results in reading information from a DNA molecule.

1.translation 2.transcription 3.transformation

11. The properties of proteins are determined...

1. secondary structure of the protein 2. primary structure of the protein

3.tertiary protein structure

12. The process by which an anticodon recognizes a codon on mRNA

13. Stages of protein biosynthesis.

1.transcription, translation 2.transformation, translation

3.transorganization, transcription

14. The anticodon of tRNA consists of UCG nucleotides. Which DNA triplet is complementary to it?

1.UUG 2. TTC 3. TCG

15. The number of tRNAs involved in translation is equal to the number:

1. mRNA codons that encode amino acids 2. mRNA molecules

3 Genes included in the DNA molecule 4. Proteins synthesized on ribosomes

16. Establish the sequence of arrangement of i-RNA nucleotides during transcription from one of the DNA strands: A-G-T-C-G

1) U 2) G 3) C 4) A 5) C

17. When a DNA molecule replicates, it produces:

1) a thread that has broken up into separate fragments of daughter molecules

2) a molecule consisting of two new DNA strands

3) a molecule, half of which consists of an mRNA strand

4) a daughter molecule consisting of one old and one new DNA strand

18. The template for the synthesis of an mRNA molecule during transcription is:

1) the entire DNA molecule 2) completely one of the chains of the DNA molecule

3) a section of one of the DNA chains

4) in some cases one of the chains of the DNA molecule, in others – the entire DNA molecule.

19. The process of self-duplication of a DNA molecule.

1.replication 2.reparation

3. reincarnation

20. During protein biosynthesis in a cell, the energy of ATP is:

1) consumed 2) stored

3) is not consumed or allocated

21. In the somatic cells of a multicellular organism:

1) different set of genes and proteins 2) same set of genes and proteins

3) the same set of genes, but a different set of proteins

4) the same set of proteins, but a different set of genes

22.. One triplet of DNA carries information about:

1) sequence of amino acids in a protein molecule

2) characteristic of the organism 3) amino acid in the molecule of the synthesized protein

4) the composition of the RNA molecule

23. Which of the processes does not occur in cells of any structure and function:

1) protein synthesis 2) metabolism 3) mitosis 4) meiosis

24. The concept of “transcription” refers to the process:

1) DNA duplication 2) mRNA synthesis on DNA

3) transfer of mRNA to ribosomes 4) creation of protein molecules on the polysome

25. A section of a DNA molecule that carries information about one protein molecule is:

1)gene 2)phenotype 3)genome 4)genotype

26. Transcription in eukaryotes occurs in:

1) cytoplasm 2) endoplasmic membrane 3) lysosomes 4) nucleus

27. Protein synthesis occurs in:

1) granular endoplasmic reticulum

2) smooth endoplasmic reticulum 3) nucleus 4) lysosomes

28. One amino acid is encoded:

1) four nucleotides 2) two nucleotides

3) one nucleotide 4) three nucleotides

29. A triplet of ATC nucleotides in a DNA molecule will correspond to a codon of an mRNA molecule:

1) TAG 2) UAG 3) UTC 4) TsAU

30. Punctuation marksgenetic code:

1. encode certain proteins 2. trigger protein synthesis

3. stop protein synthesis

31. The process of self-duplication of a DNA molecule.

1. replication 2. reparation 3. reincarnation

32. Function of mRNA in the process of biosynthesis.

1.storage of hereditary information 2.transport of AK to ribosomes

3.supplying information to ribosomes

33. The process when tRNAs bring amino acids to ribosomes.

1.transcription 2.translation 3.transformation

34. Ribosomes that synthesize the same protein molecule.

1.chromosome 2.polysome 3.megachromosome

35. The process by which amino acids form a protein molecule.

1.transcription 2.translation 3.transformation

36. Matrix synthesis reactions include...

1.DNA replication 2.transcription, translation 3.both answers are correct

37. One DNA triplet carries information about:

1.Sequences of amino acids in a protein molecule
2.Location of a specific AK in the protein chain
3. Characteristics of a specific organism
4. Amino acid included in the protein chain

38. The gene encodes information about:

1) the structure of proteins, fats and carbohydrates 2) the primary structure of protein

3) nucleotide sequences in DNA

4) amino acid sequences in 2 or more protein molecules

39. mRNA synthesis begins with:

1) separation of DNA into two strands 2) interaction of the RNA polymerase enzyme and the gene

3) gene duplication 4) gene decay into nucleotides

40. Transcription occurs:

1) in the nucleus 2) on ribosomes 3) in the cytoplasm 4) on the channels of the smooth ER

41. Protein synthesis does not occur on ribosomes in:

1) tuberculosis pathogen 2) bees 3) fly agaric 4) bacteriophage

42. During translation, the matrix for assembling the polypeptide chain of a protein is:

1) both strands of DNA 2) one of the strands of the DNA molecule

3) an mRNA molecule 4) in some cases one of the DNA chains, in others – an mRNA molecule

One of the features of proteins is their complex structural organization. All proteins have a primary, secondary and tertiary structure, and those that have two or more PCPs also have a quaternary structure (QS).

Protein primary structure (PSB) – this is the order of alternation (sequence) of amino acid residues in the PPC.

Even proteins that are identical in length and amino acid composition can be different substances. For example, from two amino acids you can make 2 different dipeptides:

With the number of amino acids equal to 20, the number of possible combinations is 210 18. And if we consider that in the PPC each amino acid can occur more than once, then the number of possible options is difficult to count.

Determination of the primary protein structure (PSB).

The PBP of proteins can be determined using phenylthiohydantoin method . This method is based on the interaction reaction phenylisothiocyanate (FITC) with α-AA. As a result, a complex of these two compounds is formed - FITZ-AK . For example, consider the peptide in order to determine its PBP, that is, the sequence of amino acid residues.

FITC interacts with the terminal amino acid (a). A complex is formed FTG-a, it is separated from the mixture and the identity of the amino acid is determined A. For example, this - asn etc. All other amino acids are sequentially separated and identified. This is a labor-intensive process. Determining the PBP of a medium-sized protein takes several months.

Priority in decoding the PSB belongs to Sengeru(1953), who discovered insulin PSB (Nobel Prize winner). The insulin molecule consists of 2 PPCs - A and B.

The A chain consists of 21 amino acids, the B chain of 30. The PPCs are connected to each other by disulfide bridges. The number of proteins whose PBP has been determined currently reaches 1500. Even small changes in the primary structure can significantly change the properties of a protein. The erythrocytes of healthy people contain HbA - when replaced in the  chain of HbA, in the 6th position glu on shaft a serious illness occurs sickle cell anemia, in which children born with this anomaly die at an early age. On the other hand, there are possible options for changing PSB, which do not affect its physicochemical and biological properties. For example, HbC contains a b-chain in the 6th position instead of glu-lys, HbC is almost no different in its properties from HbA, and people who have such Hb in their erythrocytes are practically healthy.

PSB stability is provided mainly by strong covalent peptide bonds and, secondarily, by disulfide bonds.

Protein secondary structure (PSS).

The PPCs of proteins are highly flexible and acquire a specific spatial structure or conformation. There are 2 levels of such conformation in proteins - this is the VSB and the tertiary structure (TSB).

VSB – this is the configuration of the PPC, that is, the way it is laid or twisted into some conformation, in accordance with the program embedded in the P SB.

Three main types of VSB are known:

1)  -spiral;

2) b-structure(folded layer or folded leaf);

3) a messy tangle.

-spiral .

Its model was proposed by W. Pauling. It is most likely for globular proteins. For any system, the most stable state is the one corresponding to the minimum free energy. For peptides, this state occurs when the CO– and NH– groups are connected to each other by a weak hydrogen bond. IN a -spirals The NH– group of the 1st amino acid residue interacts with the CO– group of the 4th amino acid. As a result, the peptide backbone forms a helix, each turn of which contains 3.6 AA residues.

1 spiral pitch (1 turn) = 3.6 AA = 0.54 nm, elevation angle – 26°

The twisting of the PPC occurs clockwise, that is, the spiral has a right motion. Every 5 turns (18 AC; 2.7 nm) the PPC configuration is repeated.

Stabilizing VSB primarily by hydrogen bonds, and secondly by peptide and disulfide bonds. Hydrogen bonds are 10-100 times weaker than ordinary chemical bonds; however, due to their large number, they provide a certain rigidity and compactness of the VSB. The side R-chains of the a-helix face outward and are located on opposite sides of its axis.

b -structure .

These are folded sections of the PPC, shaped like a leaf folded into an accordion. PPC layers can be parallel if both chains start from the N- or C-terminus.

If adjacent chains in a layer are oriented with opposite ends N–C and C–N, then they are called antiparallel.

parallel

antiparallel

The formation of hydrogen bonds occurs, as in the a-helix, between the CO– and NH– groups.

The existence of 4 levels of structural organization of a protein molecule has been proven.

Primary protein structure– the sequence of arrangement of amino acid residues in the polypeptide chain. In proteins, individual amino acids are linked to each other peptide bonds, arising from the interaction of a-carboxyl and a-amino groups of amino acids.

To date, the primary structure of tens of thousands of different proteins has been deciphered. To determine the primary structure of a protein, the amino acid composition is determined using hydrolysis methods. Then the chemical nature of the terminal amino acids is determined. The next step is determining the sequence of amino acids in the polypeptide chain. For this purpose, selective partial (chemical and enzymatic) hydrolysis is used. It is possible to use X-ray diffraction analysis, as well as data on the complementary nucleotide sequence of DNA.

Protein secondary structure– configuration of the polypeptide chain, i.e. a method of packaging a polypeptide chain into a specific conformation. This process does not proceed chaotically, but in accordance with the program embedded in the primary structure.

The stability of the secondary structure is ensured mainly by hydrogen bonds, but a certain contribution is made by covalent bonds - peptide and disulfide.

The most probable type of structure of globular proteins is considered a-helix. The twisting of the polypeptide chain occurs clockwise. Each protein is characterized by a certain degree of helicalization. If the hemoglobin chains are 75% helical, then pepsin is only 30%.

The type of configuration of polypeptide chains found in the proteins of hair, silk, and muscles is called b-structures. The segments of the peptide chain are arranged in a single layer, forming a figure similar to a sheet folded into an accordion. The layer can be formed by two or more peptide chains.

In nature, there are proteins whose structure does not correspond to either the β- or a-structure, for example, collagen is a fibrillar protein that makes up the bulk of connective tissue in the human and animal body.

Protein tertiary structure– spatial orientation of the polypeptide helix or the way the polypeptide chain is laid out in a certain volume. The first protein whose tertiary structure was elucidated by X-ray diffraction analysis was sperm whale myoglobin (Fig. 2).

In stabilizing the spatial structure of proteins, in addition to covalent bonds, the main role is played by non-covalent bonds (hydrogen, electrostatic interactions of charged groups, intermolecular van der Waals forces, hydrophobic interactions, etc.).

According to modern concepts, the tertiary structure of a protein, after completion of its synthesis, is formed spontaneously. The main driving force is the interaction of amino acid radicals with water molecules. In this case, non-polar hydrophobic amino acid radicals are immersed inside the protein molecule, and polar radicals are oriented towards water. The process of formation of the native spatial structure of a polypeptide chain is called folding. Proteins called chaperones. They participate in folding. A number of hereditary human diseases have been described, the development of which is associated with disturbances due to mutations in the folding process (pigmentosis, fibrosis, etc.).

Using X-ray diffraction analysis methods, the existence of levels of structural organization of the protein molecule, intermediate between the secondary and tertiary structures, has been proven. Domain is a compact globular structural unit within a polypeptide chain (Fig. 3). Many proteins have been discovered (for example, immunoglobulins), consisting of domains of different structure and functions, encoded by different genes.

All biological properties of proteins are associated with the preservation of their tertiary structure, which is called native. The protein globule is not an absolutely rigid structure: reversible movements of parts of the peptide chain are possible. These changes do not disrupt the overall conformation of the molecule. The conformation of a protein molecule is influenced by the pH of the environment, the ionic strength of the solution, and interaction with other substances. Any influences leading to disruption of the native conformation of the molecule are accompanied by partial or complete loss of the protein’s biological properties.

Quaternary protein structure- a method of laying in space individual polypeptide chains that have the same or different primary, secondary or tertiary structure, and the formation of a structurally and functionally unified macromolecular formation.

A protein molecule consisting of several polypeptide chains is called oligomer, and each chain included in it - protomer. Oligomeric proteins are often built from an even number of protomers; for example, the hemoglobin molecule consists of two a- and two b-polypeptide chains (Fig. 4).

About 5% of proteins have a quaternary structure, including hemoglobin and immunoglobulins. The subunit structure is characteristic of many enzymes.

Protein molecules that make up a protein with a quaternary structure are formed separately on ribosomes and only after completion of synthesis form a common supramolecular structure. A protein acquires biological activity only when its constituent protomers are combined. The same types of interactions take part in the stabilization of the quaternary structure as in the stabilization of the tertiary structure.

Some researchers recognize the existence of a fifth level of protein structural organization. This metabolons - polyfunctional macromolecular complexes of various enzymes that catalyze the entire pathway of substrate transformations (higher fatty acid synthetases, pyruvate dehydrogenase complex, respiratory chain).