Life Sciences I - Cell Biology Lecture 2 PDF

Life Sciences I Cell biology DNA, RNA, PROTEIN BIOSYNTHESIS Lecture 2 Assoc. Prof. dr. Agila Dauksiene  Molecular composition of cell...

Life Sciences I Cell biology DNA, RNA, PROTEIN BIOSYNTHESIS Lecture 2 Assoc. Prof. dr. Agila Dauksiene  Molecular composition of cell Cells are composed of: water, inorganic ions, carbon-containing (organic) molecules. Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. The Molecular Composition of Cells. Available from: https://www.ncbi.nlm.nih.gov/books/NBK9879/  Molecular structure of nucleic acids nucleic acids deoxyribonucleic acid (DNR) ribonucleic acid (RNR) Singh, A., & Gupta, A. (2018). Basics of Cell Biology and Biotechnology: Vol. First edition. Laxmi Publications Pvt Ltd. DNA Structure https://www.britannica.com/science/DNA Singh A, Gupta A. Basics of Cell Biology and Biotechnology. Vol First edition. Laxmi Publications Pvt Ltd; 2018. Accessed September 4, 2020. http://search.ebscohost.com/login.aspx?direct=true&db=e000xww&AN=2228695&site=ehost live  Features in DNA structure: It is a double helix. The two strands are antiparallel. These two strands are held together by hydrogen bonds. Singh A, Gupta A. Basics of Cell Biology and Biotechnology. Vol First edition. Laxmi Publications Pvt Ltd; 2018. Accessed September 4, 2020. http://search.ebscohost.com/login.aspx?direct=true&db=e000xww&AN=2228695&site=ehost live  Features in DNA structure: Adenine always pairs with thymine while guanine always pairs with cytosine. A-T pair has 2 hydrogen bonds while G-C pair has 3 hydrogen bonds. Hence, G ≡ Cis more stronger than A = T. The content of adenine is equal to the content of thymine and the content of guanine is equal to the content of cytosine. This is Chargaff’s rule, which is proved by the complementary base pairing in DNA structure. The genetic information is present only on one strand known as template strand. The double helix structure contains major and minor grooves in which proteins interact with DNA. Singh A, Gupta A. Basics of Cell Biology and Biotechnology. Vol First edition. Laxmi Publications Pvt Ltd; 2018. Accessed September 4, 2020. http://search.ebscohost.com/login.aspx?direct=true&db=e000xww&AN=2228695&site=ehost live  Structure of DNA Singh A, Gupta A. Basics of Cell Biology and Biotechnology. Vol First edition. Laxmi Publications Pvt Ltd; 2018. Accessed September 4, 2020. http://search.ebscohost.com/login.aspx?direct=true&db=e000xww&AN=2228695&site=ehost live  Chargoff Rules The base composition in DNA varied from one species to other species but in all cases the amount of adenine was equal to that of thymine (A = T). 2. The amounts of cytosine and guanine were also found to be equal (G = C). 3. The total amount of purines was equal to the total amounts of pyrimidines (A + G =C + T). 4. The AT/CG ratio varies between species. Singh A, Gupta A. Basics of Cell Biology and Biotechnology. Vol First edition. Laxmi Publications Pvt Ltd; 2018. Accessed September 4, 2020. http://search.ebscohost.com/login.aspx?direct=true&db=e000xww&AN=2228695&site=ehost live  RNA Structure Like DNA, RNA is made up of a long chain of components called ribonucleotides. The basic components of RNA are the same than for DNA with a few major differences. The pyrimidine base uracil replaces thymine and ribose replaces deoxyribose. Adenine and Uracil form a base pair formed by two hydrogen bonds. Unlike double-strandedDNA, RNA is a single-stranded molecule in many of its biological roles and has a much shorter chain of nucleotides.  (A) RNA contains the sugar ribose, which differs from deoxyribose, the sugar used in DNA, by the presence of an additional -OH group. (B) RNA contains the base uracil, which differs from thymine, the equivalent base in DNA, by the absence of a -CH3 group. (C) A short length of RNA. The phosphodiester chemical linkage between nucleotides in RNA is the same as that in DNA. Molecular Biology of the Cell. 4th edition. Alberts B, Johnson A, Lewis J, et al. New York: Garland Science; 2002.  Structure of RNA Singh A, Gupta A. Basics of Cell Biology and Biotechnology. Vol First edition. Laxmi Publications Pvt Ltd; 2018. Accessed September 4, 2020. http://search.ebscohost.com/login.aspx?direct=true&db=e000xww&AN=2228695&site=ehost live Like DNA, RNA is a linear polymer made of four different types of nucleotide subunits linked together by phosphodiester bonds. It differs from DNA chemically in two respects: (1) the nucleotides in RNA are ribonucleotides—that is, they contain the sugar ribose (hence the name ribonucleic acid) rather than deoxyribose; (2) although, like DNA, RNA contains the bases adenine (A), guanine (G), and cytosine (C), it contains the base uracil (U) instead of the thymine (T) in DNA.  ❑ Messenger RNA (mRNA) ❑ Transfer RNA (tRNA) ❑ Ribosomal RNA (rRNA) ❑ Ribozymes: The RNA molecules with catalytic activity. ❑ Small RNA molecules: RNA interference and other functions. Singh A, Gupta A. Basics of Cell Biology and Biotechnology. Vol First edition. Laxmi Publications Pvt Ltd; 2018. Accessed September 4, 2020. http://search.ebscohost.com/login.aspx?direct=true&db=e000xww&AN=2228695&site=ehost live Clark, David P.. Molecular Biology, Elsevier Science & Technology, 2009. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/kmult-ebooks/detail.action?docID=269863  Ribosomal RNA (rRNA) rRNAs are found in the ribosomes and account for 80% of the total RNA present in the cell. http://plantcellbiology.masters.grkraj.org/html/Plant_Cellular_Structures8-Ribosomes_files/image010.jpg  Ribosomal RNA (rRNA) rRNAs combine with proteins and enzymes in the cytoplasm to form ribosomes, which act as the site of protein synthesis. These complex structures travel along the mRNA molecule during translation and facilitate the assembly of amino acids to form a polypeptide chain. They interact with tRNAs and other molecules that are crucial to protein synthesis. https://cdn.britannica.com/80/780-004-BB3E8762/Synthesis-protein.jpg  Ribosomal RNA (rRNA) http://mol-biol4masters.masters.grkraj.org/html/RNA_Processing4-Processing_of_Eukaryotic_pre_rRNA_files/image004.jpg  Messenger RNA (mRNA) Messenger RNA (mRNA) is a single- stranded RNA molecule that is complementary to one of the DNA strands of a gene. The mRNA is an RNA version of the gene that leaves the cell nucleus and moves to the cytoplasm where proteins are made. During protein synthesis, an organelle called a ribosome moves along the mRNA, reads its base sequence, and uses the genetic code to translate each three-base triplet, or codon, into its corresponding amino acid. https://www.genome.gov/genetics-glossary/messenger-rna  Transfer RNA (tRNA) Transfer RNAs or tRNAs are molecules that act as temporary carriers of amino acids, bringing the appropriate amino acids to the ribosome based on the messenger RNA (mRNA) nucleotide sequence. In this way, they act as the intermediaries between nucleotide and amino acid sequences.  Transfer RNA (tRNA) codons anticodon tRNAs are ribonucleic acids and therefore capable of forming hydrogen bonds with mRNA.  Small Nuclear RNAs These molecules play a critical role in gene regulation by way of RNA splicing (during splicing, introns (non-coding regions) are removed and exons (coding regions) are joined together). snRNAs are found in the nucleus and are typically tightly bound to proteins in complexes called snRNPs (small nuclear ribonucleoproteins, sometimes pronounced "snurps"). The most abundant of these molecules are the U1, U2, U5, and U4/U6 particles, which are involved in splicing pre-mRNA to give rise to mature mRNA. Clancy, S. (2008) RNA Functions. Nature Education 1(1):102  Small Nucleolar RNAs Inside the eukaryotic nucleus, the nucleolus is the structure where rRNA processing and ribosomal assembly take place. Molecules called small nucleolar RNAs (snoRNAs) were isolated from nucleolar extracts because of their abundance in this structure. These molecules function to process rRNA molecules. Clancy, S. (2008) RNA Functions. Nature Education 1(1):102  Catalytic RNA RNAs with enzymatic (specifically, catalytic) activity, such as the self-splicing molecules, are commonly referred to as ribozymes. Ribozymes have roles in replication, mRNA processing, and splicing. By definition, these molecules can initiate their activities without the assistance of additional protein components, although they are often more efficient in vivo (Serganov & Patel, 2007). Clancy, S. (2008) RNA Functions. Nature Education 1(1):102 DNA replication https://i.ytimg.com/vi/QSTrQvp1Fyg/maxresdefault.jpg Key points: DNA replication is semiconservative. Each strand in the double helix acts as a template for synthesis of a new, complementary strand. New DNA is made by enzymes called DNA polymerases, which require a template and a primer (starter) and synthesize DNA in the 5' to 3' direction. During DNA replication, one new strand (the leading strand) is made as a continuous piece. The other (the lagging strand) is made in small pieces. DNA replication requires other enzymes in addition to DNA polymerase, including DNA primase, DNA helicase, DNA ligase, and topoisomerase.  DNA replication is semiconservative. http://blog.canacad.ac.jp/bio/BiologyIBHL1/836.html New DNA is made by enzymes called DNA polymerases http://cnx.org/content/m46073/latest/?collection=col11496/latest Replication always starts at specific locations on the DNA, which are called origins of replication and are recognized by their sequence. Specialized proteins recognize the origin, bind to this site, and open up the DNA. As the DNA opens, two Y-shaped structures called replication forks are formed, together making up what's called a replication bubble. The replication forks will move in opposite directions as replication proceeds. http://cnx.org/content/m46073/latest/?collection=col11496/latest Helicase is the first replication enzyme to load on at the origin of replication. Helicase's job is to move the replication forks forward by "unwinding" the DNA (breaking the hydrogen bonds between the nitrogenous base pairs). http://cnx.org/content/m46073/latest/?collection=col11496/latest Primers and primase DNA polymerases can only add nucleotides to the 3' end of an existing DNA strand. (They use the free -OH group found at the 3' end as a "hook," adding a nucleotide to this group in the polymerization reaction.) The problem is solved with the help of an enzyme called primase. Primase makes an RNA primer, or short stretch of nucleic acid complementary to the template, that provides a 3' end for DNA polymerase to work on. A typical primer is about five to ten nucleotides long. The primer primes DNA synthesis, i.e., gets it started. Once the RNA primer is in place, DNA polymerase "extends" it, adding nucleotides one by one to make a new DNA strand that's complementary to the template strand.  Leading and lagging strands DNA polymerases can only make DNA in the 5' to 3' direction, and this poses a problem during replication. A DNA double helix is always anti-parallel; in other words, one strand runs in the 5' to 3' direction, while the other runs in the 3' to 5' direction. This makes it necessary for the two new strands, which are also antiparallel to their templates, to be made in slightly different ways. One new strand, which runs 5' to 3' towards the replication fork, is the easy one. This strand is made continuously, because the DNA polymerase is moving in the same direction as the replication fork. This continuously synthesized strand is called the leading strand.  The other new strand, which runs 5' to 3' away from the fork, is trickier. This strand is made in fragments because, as the fork moves forward, the DNA polymerase (which is moving away from the fork) must come off and reattach on the newly exposed DNA. This tricky strand, which is made in fragments, is called the lagging strand. The small fragments are called Okazaki fragments. The gaps between DNA fragments are sealed by DNA ligase. http://blog.canacad.ac.jp/bio/BiologyIBHL1/836.html https://www.khanacademy.org/science/biology/dna-as-the-genetic-material/dna-replication/a/molecular-mechanism-of-dna-replication Summary Helicase opens up the DNA at the replication fork. Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA. Topoisomerase works at the region ahead of the replication fork to prevent supercoiling. Primase synthesizes RNA primers complementary to the DNA strand. DNA polymerase III extends the primers, adding on to the 3' end, to make the bulk of the new DNA. RNA primers are removed and replaced with DNA by DNA polymerase I. The gaps between DNA fragments are sealed by DNA ligase. http://blog.canacad.ac.jp/bio/BiologyIBHL1/836.html Prokaryotic DNA Replication Eukaryotic DNA Replication http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/DNAReplication.html https://biologywise.com/prokaryotic-vs-eukaryotic-dna-replication Protein synthesis Transcription Translation Stages of Translation in Protein Synthesis 1. Initiation: Ribosomal subunits bind to mRNA. 2. Elongation: The ribosome moves along the mRNA molecule linking amino acids and forming a polypeptide chain. 3. Termination: The ribosome reaches a stop codon, which terminates protein synthesis and releases the ribosome. Transfer RNA Transfer RNA plays a huge role in protein synthesis and translation. Its job is to translate the message within the nucleotide sequence of mRNA to a specific amino acid sequence. These sequences are joined together to form a protein. Transfer RNA is shaped like a clover leaf with three loops. It contains an amino acid attachment site on one end and a special section in the middle loop called the anticodon site. The anticodon recognizes a specific area on a mRNA called a codon.  Messenger RNA Modifications Translation occurs in the cytoplasm. After leaving the nucleus, mRNA must undergo several modifications before being translated. Sections of the mRNA that do not code for amino acids, called introns, are removed. A poly-A tail, consisting of several adenine bases, is added to one end of the mRNA, while a guanosine triphosphate cap is added to the other end. These modifications remove unneeded sections and protect the ends of the mRNA molecule. Once all modifications are complete, mRNA is ready for translation. Bailey, Regina. "Translation: Making Protein Synthesis Possible." ThoughtCo, Aug. 28, 2020, thoughtco.com/protein-synthesis-translation-373400.  Translation Initiation During translation, a small ribosomal subunit attaches to a mRNA molecule. At the same time an initiator tRNA molecule recognizes and binds to a specific codon sequence on the same mRNA molecule. A large ribosomal subunit then joins the newly formed complex. The initiator tRNA resides in one binding site of the ribosome called the P site, leaving the second binding site, the A site, open. When a new tRNA molecule recognizes the next codon sequence on the mRNA, it attaches to the open A site. A peptide bond forms connecting the amino acid of the tRNA in the P site to the amino acid of the tRNA in the A binding site. Bailey, Regina. "Translation: Making Protein Synthesis Possible." ThoughtCo, Aug. 28, 2020, thoughtco.com/protein-synthesis-translation-373400. https://www.memorangapp.com/flashcards/140164/Protein+Synthesis  Elongation As the ribosome moves along the mRNA molecule, the tRNA in the P site is released and the tRNA in the A site is translocated to the P site. The A binding site becomes vacant again until another tRNA that recognizes the new mRNA codon takes the open position. This pattern continues as molecules of tRNA are released from the complex, new tRNA molecules attach, and the amino acid chain grows. Bailey, Regina. "Translation: Making Protein Synthesis Possible." ThoughtCo, Aug. 28, 2020, thoughtco.com/protein-synthesis-translation-373400.  Termination The ribosome will translate the mRNA molecule until it reaches a termination codon on the mRNA. When this happens, the growing protein called a polypeptide chain is released from the tRNA molecule and the ribosome splits back into large and small subunits. The newly formed polypeptide chain undergoes several modifications before becoming a fully functioning protein. Proteins have a variety of functions. Some will be used in the cell membrane, while others will remain in the cytoplasm or be transported out of the cell. Many copies of a protein can be made from one mRNA molecule. This is because several ribosomes can translate the same mRNA molecule at the same time. These clusters of ribosomes that translate a single mRNA sequence are called polyribosomes or polysomes. Bailey, Regina. "Translation: Making Protein Synthesis Possible." ThoughtCo, Aug. 28, 2020, thoughtco.com/protein-synthesis-translation-373400.  Translation https://13tellge.files.wordpress.com/2011/11/rnatranslation.jpeg  Literature Rodwell V.W., & Bender D.A., & Botham K.M., & Kennelly P.J., & Weil P(Eds.), (2018). Harper's Illustrated Biochemistry, 31e. McGraw Hill. https://accessmedicine.mhmedical.com/content.aspx?bookid=2386&sectionid=187833635 Rao, N.Mallikarjuna. Medical Biochemistry, New Age International Ltd, 2006. ProQuest Ebook Central, https://ebookcentral.proquest.com/lib/kmult-ebooks/detail.action?docID=346113. Clark, David P.. Molecular Biology, Elsevier Science & Technology, 2009. ProQuest Ebook Central,. http://ebookcentral.proquest.com/lib/kmult-ebooks/detail.action?docID=269863. Singh A, Gupta A. Basics of Cell Biology and Biotechnology. Vol First edition. Laxmi Publications Pvt Ltd; 2018. Accessed September 4, 2020. http://search.ebscohost.com/login.aspx?direct=true&db=e000xww&AN=2228695&site=ehost-live https://www.khanacademy.org/science/biology/dna-as-the-genetic-material/dna-replication/a/molecular- mechanism-of-dna-replication. Bailey, Regina. "Translation: Making Protein Synthesis Possible." ThoughtCo, Aug. 28, 2020, thoughtco.com/protein-synthesis-translation-373400.  Glossary Clark, David P.. Molecular Biology, Elsevier Science & Technology, 2009. 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