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    The ribosome – a macromolecular machine par excellence

    The ribosome is the site in the cell where proteins are synthesized. Cryo-electron microscopy and X-ray crystallography have revealed the ribosome as …


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    The ribosome – a macromolecular machine par excellence


    The ribosome is the site in the cell where proteins are synthesized. Cryo-electron microscopy and X-ray crystallography have revealed the ribosome as a particle made of two subunits, each formed as an intricate mesh of RNAs and many proteins. Ligand-binding experiments followed by cryo-electron microscopy have helped to determine some of the key stages of interaction between the ribosome and the main ligand molecules.


    The ribosome – a macromolecular machine par excellence

    Source : www.sciencedirect.com

    Chapter 3. Amino Acids & Proteins – Introduction to Molecular and Cell Biology


    3.4.2 Secondary Structure

    The local folding of the polypeptide in some regions gives rise to the secondary structure of the protein. The most common are the α-helix and β-pleated sheet structures (Figure 3.10). Both structures are formed by hydrogen bonds forming between parts of the peptide backbone of the polypeptide. Specifically, the oxygen atom in the carbonyl group in one amino acid interacts with another amino acid that is four amino acids farther along the chain.


    3.4.3 Tertiary Structure

    The unique three-dimensional structure of a polypeptide is its tertiary structure (Figure 3.11). This structure is primarily due to interactions among R groups. For example, R groups with like charges are repelled by each other and those with unlike charges are attracted to each other via ionic bonds. When protein folding takes place in a watery environment, such as that found inside cells, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, while the hydrophilic R groups face out. Hydrophobic R groups also interact with each other through van der Waals forces.Interaction between cysteine side chains forms disulfide linkages, which are the only covalent bond formed during protein folding. All of these interactions determine the final three-dimensional shape of the protein. When a protein loses its three-dimensional shape, it may no longer be functional.


    3.4.4 Quaternary Structure

    In nature, some proteins are formed from several separate polypeptides, known as subunits. The interaction of these subunits forms the quaternary structure of a protein. Weak interactions between the subunits help to stabilize the overall structure. For example, silk is a fibrous protein that results from hydrogen bonding between different chains.

    The four levels of protein structure (primary, secondary, tertiary, and quaternary) are illustrated in Figure 3.1.


    3.4.5 Denaturation and Protein Folding

    If a protein is subject to changes in temperature, pH, or exposure to chemicals, it may lose its shape, a process called denaturation. The primary structure of the protein is not changed by denaturation but some or all of the folding is lost. Denaturation is often reversible, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to permanent loss of function. One example of irreversible protein denaturation is cooking an egg white. Different proteins denature under different conditions. For example, bacteria from hot springs have proteins that function at temperatures close to boiling. Although stomach acid denatures proteins as part of digestion, the digestive enzymes of the stomach retain their activity under these conditions.

    Correct folding of proteins is critical to their function. Although some proteins fold automatically, recent research has discovered that some proteins receive assistance in folding from protein helpers known as chaperones.

    Chapter 3. Amino Acids & Proteins – Introduction to Molecular and Cell Biology

    Source : rwu.pressbooks.pub

    What Are the Biomolecules of Ribosomes?

    The two types of molecule from which a ribosome is made are nucleic acid and protein. In fact, they are about 60 percent RNA, which comprises their structure, and 40 percent protein, which speeds up their work. This makes sense because the ribosome's job is to build new proteins.

    One of the most important functions of living cells is to produce the proteins necessary for an organism’s survival. Proteins give shape and structure to an organism and, as enzymes, regulate biological activity. To manufacture proteins, a cell needs to read and interpret the genetic information stored in its deoxyribonucleic acid, or DNA. The sites of cellular protein synthesis are the ribosomes, which can be free or bound. The importance of the free ribosome is that protein synthesis begins there.

    DNA and RNA

    DNA is a long molecular chain composed of alternating sugar and phosphate groups. One of four possible nitrogen-containing nucleotide bases -- A, C, T and G -- hangs off each sugar. The sequence of the bases along the DNA strand determines the sequence of amino acids that form proteins. Ribonucleic acid, or RNA, transmits a complementary copy of a portion of a DNA molecule -- a gene -- to ribosomes, which are tiny granules composed of RNA and protein. RNA resembles DNA except that its sugar groups contain an extra oxygen atom and it substitutes the U nucleotide base for DNA’s T base. The ribosomes create proteins according to the information stored in the messenger RNA, or mRNA.

    Complementary Coding

    The rules for transcribing DNA to RNA specify a correspondence between bases on the gene and bases on the mRNA. For example, an A base in a gene specifies a U base in the mRNA strand. Similarly, a gene’s T, C and G bases specify A, G, and C bases, respectively, in mRNA. The genetic information contained in mRNA takes the form of triplets of nucleotide bases called codons. For example, the DNA triplet TAA creates the RNA triplet UTT. The DNA and RNA strands therefore contain complementary, yet unique, information encoded in the sequence of nucleotide bases. Almost every triplet codes for a specific amino acid, although a few triplets specify the end of a gene. Several different triplets can code for the same amino acid.


    The cell manufactures ribosomes directly from ribosomal RNA, or rRNA, encoded by specific DNA genes. The rRNA combines with proteins to form large and small subunits. The two subunits only join during protein synthesis. In a prokaryotic cell -- that is, a cell without an organized nucleus -- the ribosome subunits float freely within the cell liquid, or cytosol. In eukaryotes, enzymes in a cell’s nucleus build ribosome subunits. The nucleus then exports the subunits to the cytosol. Some of the ribosomes may temporarily bind to a cell organelle called the endoplasmic reticulum, or ER, when building proteins, while other ribosomes remain free as they synthesize proteins.


    A free ribosome’s smaller subunit grabs hold of an mRNA strand to begin protein synthesis. The larger subunit then hooks on and begins translating each mRNA codon. This entails exposing and positioning each mRNA codon so that enzymes can identify and attach the amino acid corresponding to the current codon. A molecule of transfer RNA, or tRNA, with a complementary anti-codon locks into the larger subunit, its designated amino acid in tow. Enzymes then transfer the amino acid to the growing protein chain, expel the spent tRNA for reuse, and expose the next mRNA codon. When finished, the ribosome releases the new protein and the two subunits dissociate.

    What Are the Biomolecules of Ribosomes?

    Source : sciencing.com

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