En plu… Transcribed rRNA is bound to ribosomal proteins to form the subunits of ribosomes and acts as the physical structure that pushes mRNA and tRNA through the ribosome to process and translate them.[1]. Ribsomes can be bound to … The complex is stable under cell-like ionic conditions, consistent with functional interaction between RNAP and the 30S subunit. Modeling the Comparative Structure of Ribosomal RNAs in the 1980s; 2. Their composition can be divided into two parts – 2/3 part of r-RNA (ribosomal RNA) and 1/3 part RNP (Ribosomal protein or Ribonuclep protein). RNA consists of an unbranched single-strand polymer with many intramolecular double-stranded sections. RNA or ribonucleic acid is a polymer of nucleotides which is made up of a ribose sugar, a phosphate, and bases such as adenine, guanine, cytosine, and uracil. A refined model has been developed for the folding of 16S rRNA in the 30S subunit, based on additional constraints obtained from new experimental approaches. J Mol Biol. Structure determination of a frameshifting-primed ribosomal complex . It is commonly assumed that the function of ribosomal proteins is to stabilize specific RNA structures and to promote a compact folding of the large rRNAs. In the ribosomes of eukaryotes such as humans, the SSU contains a single small rRNA (~1800 nucleotides) while the LSU contains two small rRNAs and one molecule of large rRNA (~5000 nucleotides). Probing the rRNA environment of ribosomal protein S5 across the subunit interface and inside the 30 S subunit using tethered Fe(II). The RNA is ribonucleic acid, tRNA, rRNA and mRNA are three different types of RNA present in a cell. It has been observed that certain, Researchers found that removal of a whole, Addition of large, nonsensical RNA fragments into many parts of the 16S rRNA unit does not observably alter the function of the, While most cellular functions degrade heavily after only short period of exposure to, rRNA is one of only a few gene products present in all, Alterations to rRNA are what allow certain disease-causing, rRNA is the target of numerous clinically relevant, rRNA have been shown to be the origin of species-specific, This page was last edited on 23 December 2020, at 01:09. A low growth-rate yields lower rRNA / ribosomal synthesis rates while a higher growth rate yields a higher rRNA / ribosomal synthesis rate. 1997 Feb 14;266(1):40-50. doi: 10.1006/jmbi.1996.0780. [25], It was previously accepted that repeat rDNA sequences were identical and served as redundancies or failsafes to account for natural replication errors and point mutations. World J Gastroenterol. Learn about the structure, types, and functions of RNA. High NTP concentration has been found to be required for efficient transcription of the rrn P1 promoters. Mapping the rRNA neighborhood of the acceptor end of tRNA in the ribosome. As the building-blocks for the organelle, production of rRNA is ultimately the rate-limiting step in the synthesis of a ribosome. Typically in bacteria there are between one and fifteen copies. National Center for Biotechnology Information, Unable to load your collection due to an error, Unable to load your delegates due to an error. USA.gov. rRNA fabricates the polypeptides and provides a mechanism for decoding mRNA into amino acids and interacts with the tRNA during translation. 16S ribosomal RNA sequences have been used extensively in the classification and identification of Bacteria and Archaea. A. Ribosomal RNA analysis. Transcription. The large 50S ribosomal subunit contains two rRNA species (the 5S and 23S ribosomal RNAs). 2007 Jul;388(7):687-91. doi: 10.1515/BC.2007.077. Ceci conduit à la formation de régions localement en hélice et de régions en boucle où les bases ne sont pas appariées. The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by X-ray crystallography . The helical RNA core is highlighted by a red box. "RRNA" redirects here. In prokaryotes. Messenger RNA (mRNA)-Moves genetic information from the DNA to the ribosome, a product of transcription. Although the primary structure of rRNA sequences can vary across organisms, base-pairing within these sequences commonly forms stem-loop configurations. Biochemistry. During times of cellular glucose restriction, Anti-termination factors bind downstream of the, The NRD pathway for the 40S subunit may be independent or separate from the NRD pathway for the 60S subunit. At the transcriptional level, there are both positive and negative effectors of rRNA transcription that facilitate a cell's maintenance of homeostasis: Ribosomal RNA is quite stable in comparison to other common types of RNA and persists for longer periods of time in a healthy cellular environment. The large 50S ribosomal subunit (red) and small 30S ribosomal subunit (blue) are shown with a 200 Ã…ngstrom (20 nm) scale bar. It is an intriguing problem to understand why this is so, and its elucidation is likely to be inseparable from an understanding of the structure, function, assembly, and … In fact, the transcription of pre-RNA by RNA polymerase I accounts for about 60% of cell's total cellular RNA transcription. This results in intermolecular interactions that stabilize the subunits. Component of the 90S and 60S pre-ribosomal particles. DraperStabilization of a ribosomal RNA tertiary structure by ribosomal protein L11. A second approach uses localized hydroxyl radical cleavage from a single Fe2+ tethered to unique positions on the surface of single proteins in the 30S subunit. Once a ribosome stalls, a specialized pathway on the ribosome is initiated to target the entire complex for disassembly. RauéRibosomal proteins EL11 … Get the latest public health information from CDC: https://www.coronavirus.gov, Get the latest research information from NIH: https://www.nih.gov/coronavirus, Find NCBI SARS-CoV-2 literature, sequence, and clinical content: https://www.ncbi.nlm.nih.gov/sars-cov-2/. Both prokaryotic and eukaryotic ribosomes can be broken down into two subunits, one large and one small. Structural RNAs: A. Ribosomal RNA analysis StructRNAfinder - predicts and annotates RNA families in transcript or genome sequences. Secondary structure maps of ribosomal RNA and DNA. StructRNAfinder - predicts and annotates RNA families in transcript or genome sequences. This requires the presence of all three RNA polymerases. In molecular biology, ribosomal ribonucleic acid is the RNA component of the ribosome, and is essential for protein synthesis in all living organisms. The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by X-ray crystallography. Structure and shape of the E.coli 70S ribosome. All ribosomal proteins (including the specific sequences that bind to rRNA) have been identified. The formation of eukaryotic ribosomes is a complex process that starts with transcription of a large precursor RNA that assembles into a large 90S preribosome, which matures to finally give the 40S small subunit of the ribosome. These are transcribed by RNA polymerase I. The sites were all found to be near bases that were protected from modification by the CCA end of tRNA in earlier experiments, except for a set of E-site cleavages in domain IV and a set of A-site cleavages in the alpha-sarcin loop of domain VI. Secondary structure. rRNA is a ribozyme which carries out protein synthesis in ribosomes. To correct this, the cell allows for degradation of rRNA through the non-functional rRNA decay (NRD) pathway. Please enable it to take advantage of the complete set of features! These structures aid in considering how RNPs evolved and why they remain central to eukaryotic RNA processing. J Mol Biol. During translation of mRNA, rRNA functions to bind both mRNA and tRNA to facilitate the process of translating mRNA's codon sequence into amino acids. Ribosomal subunits were partially inactivated by chemical modification at a low level. Unlike the A and P sites, the E site contains more proteins. As shown by the image in this section, there is an internal transcribed spacer between 16S and 23S rRNA genes. The A loop is an essential RNA component of the ribosome peptidyltransferase center that directly interacts with aminoacyl (A)-site tRNA. This single tool not only displays the sequence/structural consensus alignments for each RNA family, according to Rfam database but also provides a taxonomic overview for each assigned functional RNA. Unlike messenger RNA (mRNA), it does not transmit genetic information. rRNA initiates the catalysis of protein synthesis when tRNA is sandwiched between the SSU and LSU. All sequences are available in aligned format. They serve critical roles in forming the catalytic sites of translation of mRNA. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Seventy-five residues at the C-terminus of ribosomal protein L11 are protected from trypsin digestion by the ribosomal RNA target of the protein . This site needs JavaScript to work properly. The RNA processing then begins before the transcription is complete. Alternative name(s): Ribosome biogenesis protein RRP14 ... Subunit structure i . In contrast, eukaryotes generally have many copies of the rRNA genes organized in tandem repeats. Unlike other cellular polymerases, ribosomes typically contain 50 to 60 percent RNA as an integral part of their structures. ... Y. Xing, D.E. [26] Certain variants are also expressed in a tissue-specific manner in mice.[27]. The ribosome is the structure where protein synthesis takes place. [53], Although there is far less research available on ribosomal RNA degradation in prokaryotes in comparison to eukaryotes, there has still been interest on whether bacteria follow a similar degradation scheme in comparison to the NRD in eukaryotes. 1999 Feb 19;286(2):355-64. doi: 10.1006/jmbi.1998.2483. Simple RNA Secondary and Tertiary Structure Base Pair and Unpaired Nucleotide Definitions; 1D. [16] This is followed by the folding of the pre-RNA so that it can be assembled with ribosomal proteins. The exemplary species used in the table below for their respective rRNAs are the bacterium Escherichia coli (prokaryote) and human (eukaryote). previous RNA, complex compound of high molecular weight that functions in cellular protein synthesis and replaces DNA as a carrier of genetic codes in some viruses. 2010 Dec 10;87(6):802-12. doi: 10.1016/j.ajhg.2010.11.001. Structure. (Reference: Arias-Carrasco R et al. Polypeptide chain is fabricated by translating mRNA (messenger RNA) with the aid amino acids that tRNA (transfer RNA) delivers. Jin LQ, Li JW, Wang SQ, Chao FH, Wang XW, Yuan ZQ. The comparison of almost complete 16S rRNA gene sequences has been widely used to establish taxonomic relationships between prokaryotic strains, with 98.65% similarity currently recognized as the cutoff for delineating species. The rRNAs form extensive secondary structures... Molecules of rRNA are synthesized in a specialized region of the cell nucleus called the nucleolus, which appears as a dense area within the nucleus and contains the genes that encode rRNA. (An exception is the mRNA binding activity of S1 protein.) Full-length precursor ribosomal RNA molecules were produced in vitro using as a template, a plasmid containing the yeast 35 S pre-rRNA gene under the control of the phage T3 promoter. There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). [38] The pre-5S rRNA enters the nucleolus for processing and assembly with 28S and 5.8S rRNA to form the LSU. However recently, the Asgard phyla, namely, Lokiarchaeota and Heimdallarchaeota, considered the closest archaeal relatives to Eukarya, were reported to possess two supersized ESs in their 23S rRNAs. [24] There may be one or more copies of the operon dispersed in the genome (for example, Escherichia coli has seven). It is defined as the molecular machine that catalyzes the synthesis of proteins. In prokaryotes, much work has been done to further identify the importance of rRNA in translation of mRNA. It has only been within the last decade that technical advances (specifically in the field of Cryo-EM) have allowed for preliminary investigation into ribosomal behavior in other eukaryotes. Abstract. 2005 Dec 28;11(48):7615-9. doi: 10.3748/wjg.v11.i48.7615. Structure and Evolution; 2A. 2017 May 5;45(8):4958-4971. doi: 10.1093/nar/gkx112. CR-I, CR-IV, and CR-V are colored in slate, orange, and cyan, respectively. 1 256. [14] In 16s rRNA, this is thought to occur when certain nucleotides in the rRNA appear to alternate base pairing between one nucleotide or another, forming a "switch" that alters the rRNA's conformation. S units of the subunits (or the rRNAs) cannot simply be added because they represent measures of sedimentation rate rather than of mass. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and a phosphate group. The secondary structure of SSU rRNA contains 4 distinct domains—the 5', central, 3' major and 3' minor domains. [1] Ribosomal RNA is the predominant form of RNA found in most cells; it makes up about 80% of cellular RNA despite never being translated into proteins itself. These interactions along with the association of the small and large ribosomal subunits result in a functioning ribosome capable of synthesizing proteins.[3]. Additional information about the … As information about ribosomal proteins and their RNA targets accumulates, we can ask whether stabilization of specific or u… The nt units can be added as these represent the integer number of units in the linear rRNA polymers (for example, the total length of the human rRNA = 7216 nt). Ribosomal RNA-processing protein 14. La structure de l'ARN décrit l'arrangement des paires de bases et de la conformation de l'ARN en trois dimensions. (A) Two orthogonal views of the overall structure of the Nme1 RNA. The A loop is highly conserved and contains a ubiquitous 2′- O -methyl ribose modification at position U2552. This assumption has been accepted largely by default, as no other specific role (e.g., substrate binding or catalysis) has been unambiguously assigned to a ribosomal protein. The ribosomal proteins and rRNAs are arranged into two distinct ribosomal pieces of different size, known generally as the large and small subunit of the ribosome. Ribosomes consist of 2 subunits of unequally sized rRNA, and the sizes are measured in terms of an “S” value (Svedberg or sedimentation unit): Based on a measure of sedimentation velocity in a centrifuge (higher “S” value = faster sedimentation = greater mass) Therefore, “S” values are not additive. Every cell has a 16S rRNA gene as the ribosomal RNA (rRNA) is an integral part of the ribosome, which is responsible for making cellular proteins. Einerhand, J. Teixido, R.J. Planta, J.P. Ballesta, H.A. Many differences were found between eukaryotic and prokaryotic rRNA degradation, leading researchers to believe that the two degrade using different pathways. [4] There are four types of rRNA in eukaryotes: 3 species in the LSU and 1 in the SSU. [34] This process is referred to as the "maturation" phase of the rRNA lifecycle. GAC RNA structures in the crystal and cocrystals are the same. Cleavage was detected in domains IV, V, and VI of 23S rRNA, but not in 5S or 16S rRNA. Ribosomal ribonucleic acid (rRNA) is the type of RNA that is part of the ribosomes.  |  The structure of rRNA is able to drastically change to affect tRNA binding to the ribosome during translation of other mRNAs. Ribosomal RNA (rRNA) Structure. The secondary structure of SSU rRNA contains 4 distinct domains—the 5', central, 3' major and 3' minor domains. STRUCTURE OF RIBOSOMAL RNA 121 and 26S or 28S rRNA. For the 50S subunit, the 23S (dark red) and 5S (orange red) rRNAs and the ribosomal proteins (pink) are shown. 50S further comprises 5S subunit of RNA(comprising almost 120 nucleotides) along with subunits of 23S RNA (almost 2900 nucleotides) and 34 protein subunits. [23], Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are typically organized as a co-transcribed operon. Deregulation of Pol I transcription perturbs normal cell growth, leading to cell death or uncontrolled cell growth and proliferation, potentially resulting in developmental defects or cancer in mammals [ 83 – 86 ]. Nucleotide Frequency Data. RNA consists of ribose nucleotides and the nitrogenous bases adenine, guanine, cytosine, and uracil. The P1 promoter is specifically responsible for regulating rRNA synthesis during moderate to high bacterial growth rates. It is largely made up of specialized RNA known as ribosomal RNA (rRNA) as well as dozens of distinct proteins (the exact number varies slightly between species). One set of constraints comes from hydroxyl radical footprinting of each of the individual 30S ribosomal proteins, using free Fe(2+)-EDTA compl … Ribosomal RNA organizes into two ribosomal subunits: the large ribosomal subunit (LSU) and small ribosomal subunit (SSU). Fig. 1974 Oct 25; 89 (2):379–395. Ribosomal ribonucleic acid (ribosomal RNA or rRNA) helps to form the ribosome itself. A model of the secondary structure for the 5' domain (500-800 nucleotides) is shown. Modeling the Comparative Structure of Ribosomal RNAs in the 1980s; 2. Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle. NIH [11] Phylogenic information derived from the 16s rRNA is currently used as the main method of delineation between similar prokaryotic species by calculating nucleotide similarity. J Mol Biol. The mRNA carries instructions that dictate the amino acid sequences of proteins. For the Love of Physics - Walter Lewin - May 16, 2011 - Duration: 1:01:26.  |  (2018) 19: 55). COVID-19 is an emerging, rapidly evolving situation. Show more details Hide details. rRNA - Ribosomal RNA and proteins form the ribosome. 5S rRNA is transcribed by RNA polymerase III. Ribosomal RNA, also known as rRNA, is a significant component of the ribosome. In prokaryotes a small 30S ribosomal subunit contains the 16S ribosomal RNA. Article Download PDF View Record in Scopus Google Scholar. For example, it has been found that the A site consists primarily of 16S rRNA. Ribosomal RNA (rRNA)The mammalian ribosome contains two majornucleoprotein subunits—a larger one with a molecularweight of 2.8 x 106 (60S) and a smaller subunit with amolecular weight of 1.4 x 106 (40S). [46][47][48], In prokaryotic cells, each rRNA gene or operon is transcribed into a single RNA precursor that includes 16S, 23S, 5S rRNA and tRNA sequences along with transcribed spacers. Each nucleotide is … The backbone of RNA is formed by 3′, 5′-phosphodiester bonds, the sugar is ribose, and the nucleobase is thymine. A model of the secondary structure for … Since they have their active part composed of sub-structures of RNA, they are also termed … [17] The basic and aromatic residues found within the primary structure of rRNA allow for favorable stacking interactions and attraction to ribosomal proteins, creating a cross-linking effect between the backbone of rRNA and other components of the ribosomal unit. 1995 Jun 2; 249 (2):319–331. J. Mol. The first spacer corresponds to the one found in bacteria and archaea, and the other spacer is an insertion into what was the 23S rRNA in prokaryotes. These ribosomal proteins contain basic residues(as opposed to acidic residues) and aromatic … Ribosomal RNA synthesis by Pol I is crucially dependent upon nutrient availability and drives ribosome biogenesis, a process important for cell growth and proliferation [80–82]. An increased rRNA concentration serves as a negative feedback mechanism to ribosome synthesis. RNA. Simple RNA Secondary and Tertiary Structure Base Pair and Unpaired Nucleotide Definitions; 1D. In Prokaryotes, rRNA incorporation occurs in the cytoplasm due to the lack of membrane-bound organelles. Upon going under more maturation steps and subsequent exit from the nucleolus into the cytoplasm, these particles combine to form the ribosomes. Ribosomal RNA's integration and assembly into ribosomes begins with their folding, modification, processing and assembly with ribosomal proteins to form the two ribosomal subunits, the LSU and the SSU. Many of these variations are palindromic sequences and potential errors due to replication. Because of these configurations, rRNA can form tight and specific interactions with ribosomal proteins to form ribosomal subunits. Ribosomal RNA … In the SSU, the mRNA interacts with the anticodons of the tRNA. Ribosomal RNA (rRNA): Structure and Functions. Similarly, like the A site, the P site primarily contains rRNA with few proteins. In the P site, through the observation of crystal structures it has been shown the 3' end of 16s rRNA can fold into the site as if a molecule of mRNA. SSU and LSU rRNA sequences are widely used for study of evolutionary relationships among organisms, since they are of ancient origin[10], are found in all known forms of life and are resistant to horizontal gene transfer. RNA tertiary structure has been less extensively studied with respect to its primary or secondary structure, with the added challenge that prediction of 3D structure is dependent on, and significantly more difficult than, determining the 2D base pairings. Stabilization of a ribosomal RNA tertiary structure by ribosomal protein L11. This folding is catalyzed by endo- and exonucleases, RNA helicases, GTPases and ATPases. Methods: Structure Prediction with Comparative Sequence Analysis; 1E. All three RNA types consist of a single-stranded chain of nucleotides. 1991 Jun;73(6):631-8. doi: 10.1016/0300-9084(91)90042-y. (B) Secondary structure diagram of the Nme1 RNA. Once assembled into functional units, ribosomal RNA within ribosomes are stable in the stationary phase of the cell life cycle for many hours. The higher-order structure of the 5'-external transcribed spacer (5' ETS) sequence in the 35S pre-rRNA molecule was … Ribosomes are composed of approximately 60% rRNA and 40% ribosomal proteins by mass. The modifications that occur during maturation of rRNA have been found to contribute directly to control of gene expression by providing physical regulation of translational access of tRNA and mRNA. Base Pairs. J Mol Biol. Aminoglycoside antibiotics that bind to 30S ribosomal A-site RNA cause misreading of the genetic code and inhibit translocation. The peptidyl transferase center, for example, is formed by nucleotides from the 23S rRNA subunit. During processing reactions, the rRNAs and tRNAs are released as separate molecules.[49]. The 3' end of the 16S ribosomal RNA (in a ribosome) recognizes a sequence on the 5' end of mRNA called the Shine-Dalgarno sequence. Active, partially modified subunits were separated from inactive ones by binding 3'-biotinderivatized tRNA to the 30S subunits and captured with streptavidin beads. The structure places the RNAP RNA exit site close to … We initially intended to capture a 0 frame, pre-frameshift ribosomal complex by first introducing a stop codon in place of the second codon of the slippery site (U_UUA_AAC to U_UUA_UAA), 7 8. The secondary structure of SSU rRNA contains 4 distinct domains -- the 5', central, 3' major and 3' minor domains. Demo et al. They are thought to form stabilizing complexes with RNA polymerase and the promoters. A ribosome has three of these binding sites called the A, P and E sites: A single mRNA can be translated simultaneously by multiple ribosomes. Lectures by Walter Lewin. The ribosomal rRNA forms complex three-dimensional structures that combine with polypeptides to create ribosomes, which are the organelles responsible for protein synthesis. Apart from various protein elements that interact with tRNA at this site, it is hypothesized that if these proteins were removed without altering ribosomal structure, the site would continue to function normally. Because of the vital role rRNA plays in the cell physiology of prokaryotes, there is much overlap in rRNA regulation mechanisms. Base Pairs. rRNA was once known to be the key structural component of ribosomes, but its actually found to be a catalytic element for protein synthesis. A eukaryotic SSU contains the 18S rRNA subunit, which also contains ESs. And you also have things called microRNA, which are short chains of RNA, which could be used to regulate the translation of other RNA molecules. One set of constraints comes from hydroxyl radical footprinting of each of the individual 30S ribosomal proteins, using free Fe(2+)-EDTA complex. Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs. I. The ribosome consists of more than 60% ribosomal RNA; these are made up of 3 ncRNAs in prokaryotes and 4 ncRNAs in eukaryotes. The ribosomes serve as a platform for decoding the mRNA. [29] The genes coding for 18S, 28S and 5.8S rRNA are located in the nucleolus organizer region and are transcribed into large precursor rRNA (pre-rRNA) molecules by RNA polymerase I. This is called a polysome. Ribosomal RNAs catalyse the translation of nucleotide sequences to protein. Owing to steric hindrance caused by the 2'-OH groups of ribose, the double-stranded RNA cannot be formed. SAE. Ribosomal RNA synthesis by Pol I is crucially dependent upon nutrient availability and drives ribosome biogenesis, a process important for cell growth and proliferation [80–82]. Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. examined the structure of the E. coli 30S ribosomal subunit complexed to the core RNA polymerase. When rRNA sequencing is altered, cells have been found to become compromised and quickly cease normal function. phenylalanine, tyrosine and tryptophan) allowing them to form chemical interactions with their associated RNA regions, such as stacking interactions. The exact details of how the folding proteins bind to the rRNA and how correct folding is achieved remains unknown. Conserved GTPase center of 23 S ribosomal RNA characteristics are important in evolution, thus taxonomy and medicine: and. 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[ 18 ribosomal rna structure Joanna L 1... Messenger RNA ( mRNA ) -Moves genetic information hindrance caused by the rRNA subsequently endo-! Groups of ribose, and VI of 23S rRNA normal function contains the 5S 5.8S.. [ 27 ] the pre-RNA so that it can be assembled with ribosomal.... That are unmodified in the total population essential to ribosome function for this area inactivated! This area, 2011 - Duration: 1:01:26 tRNA interacts with aminoacyl ( a ) orthogonal! Jun 2 ; 249 ( 2 ):355-64. doi: 10.1042/BST0360619 ( ). Spectroscopy, and Functions:26-40. doi: 10.1093/nar/gkx112 36 ( Pt 4 ):619-24. doi: 10.1017/s1355838200991659 Yuan ZQ to. 70S, where each one comprises 30S ( small ) and 50S ( large ) subunits. [ ]. Prokaryotic and eukaryotic ribosomes can be bound to … structure of the oldest discovered to ribosome. A pre-40S ribosome the Love of Physics - Walter Lewin - May 16, 2011 - Duration: 1:01:26 into! 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