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Ch. 16 and 17 (Viral DNA (Structural DNA Model (Base Pairing to a Template…

- - - - The two strands are complementary and each stores the information necessary to reconstruct the other.
      - When a cell copies a DNA molecule, each strand serves as a template for ordering nucleotides into a new, complementary strand.
      - Nucleotides line up long the template strand according to the base pairing rules and are linked to form new strands.
      - Watson and Cricks model predicts that when a double helix replicates, each of the two daughter molecules will have one old strand, from the parental molecule and one newly made strand.
      - The semiconservative model can be distinguished from a conservative model of replication in which two parental strands somehow come back together after the process.
      - DNA Replication
        
        The replication of chromosomal DNA begins at particular sites called origins of replication, short stretches of DNA that have a specific sequence of nucleotides.
        
        The E. coli chromosome is a circular and has a single origin.
        
        Proteins that initiate DNA replication recognize this sequence and attach to the DNA, separating the two strands and opening up a replication "bubble".
        
        Replication of DNA then proceeds in both directions until the entire molecule is copied.
        
        A eukaryotic chromosome may have hundreds or even a few thousand replication origins.
        
        As in bacteria, eukaryotic DNA replication proceeds in both directions from each origin.
        
        At the end of a replication bubble is a replication fork, a Y-shaped region where the parental strands of DNA are being unwound.
        
        Helicases are enzymes that untwist the double helix at the replication fork, separating the two parental strands and making them available as template strands.
        
        After the parental strands separate, single-stranded binding proteins bind to the unpaired DNA strands, keeping them from re-pairing.
        
        The untwisting of the double helix causes tighter twisting and strain ahead of the replication fork.
        
        Topoisomerase is an enzyme that helps relieve this strain by breaking, swiveling, and rejoining DNA strands.
        
        Synthesizing a New DNA Strand
        
        The initial nucleotide chain that is produces during DNA synthesis is actually a short stretch of RNA, not DNA.
        
        The RNA chain is called a primer and is synthesized by the enzyme primase.
        
        Primase starts a complementary RNA chain with a single RNA nucleotide and addsRNA nucleotides one at a time, using the parental DNA strand as a template.
        
        The new DNA strand will start from the 3' end of the RNA primer.
        
        Enzymes called DNA polymerase catalyze the synthesis of new DNA by adding nucleotides to the 3' end of a preexisting chain.
        
        Most DNA polymerases require a primer and a DNA template strand, along which complementary DNA nucleotides are lined up.
        
        Each nucleotide to be added to a growing DNA strand consists of a sugar attached to a base and to the three phosphate groups.
        
        The nucleotides used for DNA synthesis are chemically reactive because their triphosphate taels have an unstable cluster of negative charge.
        
        DNA polymerase catalyzes the addition of each monomer via dehydration reaction.
        
        Antiparallel Elongation
        
        Two strands of DNA in a double helix are antiparallel, meaning they are oriented in opposite directions to each other.
        
        New strands formed during DNA replication must also be antiparallel to their template strands.
        
        The antiparallel arrangement of the double helix has an effect on how replication occurs.
        
        DNA polymerases can add nucleotides only to the free 3' end of a primer or growing DNA strand, never to the 5' end.
        
        A new DNA strand can elongate only in the 5'---> 3' direction.
        
        Along one template strand, DNA polymerase III can synthesize a complementary strand continuously by elongation the new DNA in the mandatory 5' ---> 3' direction.
        
        DNA polymerase III remains in the replication fork on the template strand and continuously adds nucleotides the new complementary strand as the fork progresses.
        
        The DNA strand made by this mechanism is a leading strand.
        
        To elongate the other new strand of DNA in the mandatory 5' --> 3' direction, DNA polymerase III must work along the other template strand in the direction away form the replication fork.
        
        The DNA strand elongating in this direction is called the lagging strand.
        
        The lagging strand is synthesized discontinuously as a series of segments.
        
        The segments of lagging strand are called Okazaki fragments.
        
        DNA ligase joins the sugar-phosphate backbones of all the Okazaki fragments into a continuous DNA strand.
- - - - The main component of the genome in most bacteria is one double stranded, circular DNA molecule that is associated with a small amount of protein.
      - Bacterial chromosomes are different from eukaryotic chromosome, which consist of one linear DNA molecule associated with a large amount of protein.
      - Within a bacterium, certain proteins cause the chromosome to coil and "supercoil", densely packing it so that it fills only part of the cell.
      - Unlike the nucleus of eukaryotic cell, this dense region of DNA in a bacterium, called nucleoid, is not bounded by membrane.
      - Each eukaryotic chromosome contains a single linear DNA double helix.
      - In the cell, eukaryotic DNA is combined with a large amount of protein.
      - Together, this complex of DNA and protein, called chromatin, fits into the nucleus through an elaborate, multilevel system of packing.
      - Chromatin undergoes striking changes in its degree of packing during the course of the cell.
      - During interphase, the centromeres and telomeres of chromosomes, exist in a highly condensed state similar to that seen in a metaphase chromosome.
      - This type of interphase chromatin is called heterochromatin, to distinguish it form the less compacted, more dispersed euchromatin.
      - Due to its compaction, heterochromatin DNA is inaccessible to the machinery in the cell responsible for transcribing the genetic information coded in the DNA.
      - The looser packing of euchromatin makes its DNA accessible to the machinery, so the genes present can be transcribed.
      - Transcription and Translation
        
        Genes provide the instructions for making specific proteins but a gene doesn't build a protein directly.
        
        The bridge between DNA and protein synthesis is the nucleic acid RNA.
        
        RNA is chemically similar to DNA except that it contains robes instead of deoxyribose as its sugar and has the nitrogenous base uracil rather than thymine.
        
        Each nucleotide along a DNA strand has A, G, C, or T as its base and each nucleotide along an RNA strand has A, G, C, or U as its base.
        
        Transcription is the synthesis of RNA using information in the DNA.
        
        The two nucleic acids are written in different forms of the same language and the information is simply transcribed or rewritten from DNA to RNA.
        
        It can also serve as a template for assembling a complementary sequence of RNA nucleotides.
        
        For a protein-coding gene, the resulting RNA molecules is a faithful transcript of the gene's protein building instructions.
        
        The RNA molecule called messenger RNA (mRNA) because it carries a genetic message from the DNA to the protein-synthesizing machinery of the cell.
        
        Translation is the synthesis of a polypeptide using the information in the mRNA.
        
        During the stage, there is a change: the cell must translate the nucleotide sequence of an mRNA molecule into the amino acid sequence of a polypeptide.
        
        The sites of translation are ribosomes, molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains.
        
        Transcription and translation occurs in all organisms.
        
        The basic mechanics of transcription and translation are similar for bacteria and eukaryotes, but there is a difference in the flow of genetic information within the cells.
        
        Bacteria do not have nuclei. Therefore, nuclear membranes don't separate bacterial DNA and mRNA from ribosomes and the other protein-synthesizing equipment.
        
        Transcription occurs in the nucleus, but the mRNA myst be transported to the cytoplasm for the translation.
        
        Before eukaryote RNA transcripts from protein-coding genes can leave the nucleus. they are modified in various ways to produce the final, functional mRNA.
        
        The transcription of a protein-coding eukaryotic gene results in pre-mRNA, and further processing yields the finished mRNA.
        
        The initial RNA transcript from any gene, including those specifying RNA that is not translated into protein, is called primary transcript.
        
        Codons: Triplets of Nucleotides
        
        Triplets of nucleotide bases are the smallest units of uniform length that can code for all the amino acids.
        
        Experiments have verified that the flow of information from gene to protein is based on a triplet code: the genetic instructions for polypeptide chain are written in the DNA as a series of nonoverlapping, three-nucleotide words.
        
        The series of words in a gene is transcribed into a complementary series of non overlapping, three nucleotide words in mRNA which is then translated into a chain of amino acids.
        
        During transcription, the gene determines the sequence of nucleotide bases along the length of the RNA molecule that is being synthesized.
        
        For each gene, only one of the two DNA strands is transcribed. The strand is called template strand because it provides the pattern, or template, for the sequence of nucleotides in an RNA transcript.
        
        Farther along on the same chromosomal DNA molecule, the opposite strand may function as the template for a different gene.
        
        The strand that is used as the template is determined by the orientation of the enzyme that transcribes genes, which in turn depends on the particular DNA sequences associated with that gene.
        
        An mRNA molecule is complementary rather than identical to its DNA template because RNA nucleotides are assembled on the template according to base-paring rules.
        
        The pairs are similar to those that form during DNA replication, except that U pairs with A and the mRNA nucleotides contain ribose instead of deoxyribose.
        
        The mRNA nucleotides triplets are called codons, and they are customarily written in the 5' ---> 3' direction.
        
        The term codon is also used for the DNA nucleotide triplets along the nontemplate strand.
        
        These codons are complementary to the template strand and thus identical in sequence to the mRNA. except that they have a T wherever there is a U in the mRNA.
        
        The nontemplate DNA strand is called the coding strand; the sequence of the coding strand is used when a gene's sequence is reported.
        
        During translation, the sequence of codons along an mRNA molecule is decoded, or translated into a sequence of amino acids making up a polypeptide chain.
        
        The codons are read by the translation machinery in the 5' --> 3' direction along the mRNA.
        
        Molecular Components of Transcription
        
        Messenger RNA, the carrier of information from DNA to the cell's protein-synthesizing machinery, is transcribed from the template strand of a gene.
        
        An enzyme called an RNA polymerase pries the two strands DNA apart and joins together RNA nucleotides complementary to the DNA template strand, elongating the RNA polynucleotide.
        
        Like the DNA polymerases that function in DNA replication, RNA polymerases can assemble a polynucloetide only in its 5' ---> 3' direction, adding onto its 3' end.
        
        RNA polymerases are able to start a chain from scratch; they don't need to add the first nucleotide onto a pre-existing primer.
        
        Specific sequences of nucleotides along the DNA mark where transcription of a gene begins and ends.
        
        The DNA sequence where RNA polymerase attaches and initiates transcription known as promoter; in bacteria, the sequence that signals the end of transcription called terminator.
        
        The stretch of DNA downstream from the promoter that is transcribed into an RNA molecule called transcription unit.
        
        RNA Polymerase Binding and Initiation of Transcription
        
        The promoter of a gene includes within it the transcription start point, the nucleotide where RNA polymerase actually begins synthesis of the mRNA and extends several dozen or so nucleotide pairs upstream from the start point.
        
        RNA polymerase binds in a precise location and orientation on the promoter. This determines where transcription starts and which of the strands is used as the template.
        
        Certain sections of a promoter are important for binding RNA polymerase in a way that ensures that transcription will begin at the right place.
        
        In bacteria, the RNA polymerase itself specifically recognizes and binds to the promoter.
        
        In eukaryotes, a collection of proteins called transcription factors mediate the binding of RNA polymerase and the initiation of transcription.
        
        The whole complex of transcription factors and RNA polymerase II bound to the promoter is called a transcription initiation complex.
        
        The pairs are similar to those that form during DNA replication, except that U Paris with A and the mRNA nucleotides contain ribose instead of deoxyribose.
        
        The RNA molecule is synthesized in an antiparallel direction to the template strand of DNA.
- - - - The final stage of translation is termination. Elongation continues until a stop codon in the mRNA reaches the A site.
      - The nucleotide base triplets UAG, UAA and UGA don't code for amino acids but act as signals to stop translation.
      - A release factor binds to the stop codon in the A site and causes the addition of a water molecule instead of an amino acid to the polypeptide chain.
      - The reaction breaks the bond between the completed polypeptide and the tRNA in the P site, releasing the polypeptide through exit tunnel of the ribosome's large subunit.
      - The breakdown of translation assembly requires the hydrolysis of two or more GTP molecules.
      - Targeting Polypeptides to a Specific Locations
        
        Free ribosomes are suspended in the cytosol and mostly synthesize proteins that stay in the cytosol and function there.
        
        Bound ribosomes make proteins endomembrane system as well as proteins secreted from the cell.
        
        Polypeptide synthesis always begins in the cytosol as a free ribosome starts to translate an mRNA molecule.
        
        The process continues to completion. The polypeptides of proteins destines for the endomembrane system or for secretion are marked by a signal peptide, that targets the protein to the ER.
        
        The signal peptide, a sequence of about 20 amino acids at or near the leading end of the polypeptide, is recognized as it emerges from the ribosomes by a protein-RNA complex called a signal-recognition particle (SRP).
        
        The particle escorts the ribosomes to a receptor protein built into the ER membrane.
        
        Polypeptide synthesis continues and growing polypeptide snakes across the membrane into the ER lumen via protein pore.
        
        The rest of the completed polypeptide, is released into solution within the ER protein.
        
        Making Multiple Polypeptides in Bacteria and Eukaryotes
        
        A single ribosome can make an average sized polypeptide in less than a minute.
        
        In both bacteria and eukaryotes, multiple ribosomes translate an mRNA at the same time.
        
        Once a ribosome is far past the start codon, a second ribosome can attach to the mRNA, resulting in a number of ribosomes trailing along the mRNA.
        
        Such strings of ribosomes called polyribosomes can be seen with an electron microscope.
        
        The most important difference between bacteria and eukaryotes is that bacterial cell's lack of compartmental organization.
        
        The eukaryotes cell's nuclear envelope segregates transcription from translatopn and provides a compartment for extensive RNA processing.
        
        Mutations Can Affect Protein Structure and Function
        
        Mutations are responsible for the huge diversity in genes found among organisms because mutations are ultimate source of new genes.
        
        Small-scale mutations of one or a few nucleotide pairs, including point mutations, changes in a single nucleotide pair of a gene.
        
        If point mutation occurs in a gamete or in a cell that gives rise to gametes, it may be transmitted to offspring and to future generations.
        
        If the mutation has adverse effect on the phenotype of the person, the mutant condition is a genetic disorder or hereditary disease.
        
        The change in a single nucleotide in the DNA's template strand leads to an altered mRNA and the production of an abnormal protein.
        
        Substitutions
        
        A nucleotide-pair substitution is the replacement of one nucleotide and its partner with another pair of nucleotides.
        
        Some substitutions have no effect on the encoded protein.
        
        A change in a nucleotide pair may transform one codon into another that is translated into the same amino acid.
        
        The change is an example of a silent mutation, which has no effect on the phenotype.
        
        Some silent mutations may affect where or at what level the gene gets expressed, even though the actual protein is the same.
        
        Substitutions that change one amino acid to another are called missense mutations.
        
        Nucleotide-pair substitutions of greatest interest are those that cause a major change in a protein.
        
        Substitution mutations are usually missense mutations; the altered codon still codes for an amino acid.
        
        A point mutation can also change a codon for an amino acid into a stop codon. This is called a nonsense mutation and it causes translation to be determined prematurely.
        
        Insertions and Deletions
        
        Insertions and deletions are additions or losses of nucleotide pairs in a gene.
        
        These mutations have a disastrous effect on the resulting protein more often than substitutions do.
        
        Insertion and deletion of nucleotides may alter the reading frame of the genetic message, the triplet grouping of nucleotides on the mRNA that is read during translation.
        
        A mutation called frameshift mutation, occurs whenever the number of nucleotides inserted or deleted is not a multiple of three.
        
        All nucleotides downstream of the deletion of insertion will be improperly grouped into codons; resulting in extensive missense mutations.
        
        Insertions and deletions also occur outside of coding regions and can affect how the gene is expressed.
- - - - RNA splicing is where large portions of the RNA molecules are removed and the remaining portions are connected.
      - The noncoding segments of nucleic acid that lie between coding regions are called intervening sequences, or introns.
      - The other regions are called exons, because they are expressed by being translated into amino acid sequences.
      - The terms intron and exon are used for both RNA sequences and the DNA sequences that specify them.
      - In a primary transcript from a gene, RNA polymerase II transcribes both introns and exons from the DNA, but the mRNA molecule that enters the cytoplasm.
      - The removal of introns is accomplished by a large complex made of proteins and small RNAs called spliceosome.
      - The complex binds to several nucleotide sequences along an intron. The intron is released and the spliceosome joins together the two exons that flanked the intron.
      - Ribozymes
        
        The idea of a catalytic role for the RNAs in the spliceosome arose from the discovery of ribozymes, RNA molecules that function as enzymes.
        
        The intron RNA functions as a ribozyme and catalyzes its own excision.
        
        Three properties of RNA enable some RNA molecules to function as enzymes. First, RNA is single stranded, a region of an RNA molecule may base-pair, in an antiparallel arrangement, with a complementary region elsewhere in the same molecule. Second, certain amino acids in an enzymatic protein, some of the bases in RNA contain functional groups that participate in catalysis. Third, the ability of RNA to hydrogen bond with other nucleic acid molecules adds specificity to its catalytic activity.
        
        The Functional and Evolutionary Importance of Introns
        
        A single gene can encode more than one kind of polypeptide.
        
        Many genes are known to give rise to two or more different polypeptides, depending on which segments are treated as exons during RNA processing called alternative RNA splicing.
        
        Proteins often have a modular architecture consisting of discrete structural and functional regions called domains.
        
        The presence of introns in a gene may facilitate the evolution of new and potentially beneficial proteins as a result of exon shuffling.
        
        Introns increase the probability of crossing over between the exons of alleles of a gene- simply by providing more terrain for crossovers without interrupting coding sequences.
        
        Transfer RNA (tRNA)
        
        In the process of translation, a cell "reads" a genetic message and builds a polypeptide accordingly.
        
        The message is a series of codons along an mRNA molecule and the translator is called a transfer RNA (tRNA).
        
        The function of a tRNA is to transfer an amino acid from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome.
        
        The key to translating a genetic message into a specific amino acid sequence is the fact that each tRNA molecule enables translation of a given mRNA codon into a certain amino acid.
        
        It is possible becuase a tRNA bears a specific amino acid at one end of its three-dimensional structure, while at the other end is a nucleotide triplet that can base-pair with complementary codon on mRNA.
        
        The tRNA twists and folds into a compact three-dimensional structure that is L-shaped, with the 5' and 3' ends of the linear tRNA both located near one end of the structure.
        
        The protruding 3' end acts as the attachment site for an amino acid. The loop extending from the other end of L includes the anticodon.
        
        The anticodon is the particular nucleotide triplet that base-pairs to a specific mRNA codon. The structure of a tRNA molecule fits its function.
        
        Anticodons are written 3' --> 5' to align properly with codons written 5' --> 3'.
        
        The tRNA that base-pairs with this codon by hydrogen bonding has 3'-CCG-5' as its anticodon and carries glycine at its other end.
        
        As an mRNA molecule is moved through a ribosome, glycine will be added to the polypeptide chain whenever the codon 5'-GCG-3' is presented for translation.
        
        Codon by codon, the genetic message is translated as tRNAs position each amino acid in the order prescribed and the ribosome adds that amino acid onto the growing polypeptide chain.
        
        In a eukaryotic cell, tRNA is made in the nucleus and then travels to the cytoplasm, where it will participate in the process of translation.
        
        In both bacterial and eukaryotic cells, each tRNA molecule is used repeatedly, picking up its designated amino acid in the cytosol, depositing this cargo onto a polypeptide chain at the ribosome, and then leaving the ribosome, ready to pick up another of the same amino acid.
        
        The accurate translation of a genetic message requires two instances of molecular recognition. A tRNA that binds to an mRNA codon specifying a particular amino acid must carry that amino acid to the ribosome.
        
        The Structure and Function of Ribosomes
        
        Ribosomes facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis.
        
        A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more ribosomal RNAs (rRNAs).
        
        Ribosomal RNA genes are transcribed and the RNA is processed and assembled with proteins imported imported from the cytoplasm.
        
        Completed ribosomal subunits are then exported via nuclear pores to the cytoplasm.
        
        In both bacteria and eukaryotes, a largeand a small subunit join to form a functional ribosome only when attached to an mRNA molecule.
        
        The structure of a ribosome reflects its function of bringing mRNA together with tRNAs carrying amino acids.
        
        Each ribosome has three binding sites for tRNA.
        
        The P site holds the tRNA carrying the growing polypeptide chain, while the A site holds the tRNA carrying the next amino acid to be added to the chain.
        
        Discharged tRNAs leave the ribosome from the E site. The ribosome holds the tRNA and mRNA in close proximity and positions the new amino acid so that it can be added to the carboxyl end of the growing polypeptide.
        
        It then catalyzes the formation of the peptide bond. As the polypeptide becomes longer, it passes through an exit tunnel in the ribosome's large subunit.