Expression of Biological information 123 by MDM NASHIMAH HABEEB https://padlet.com/MadamNash/Chap6_123 Sharing information platform en-us 2021-09-24 01:51:16 UTC 2023-05-15 00:51:44 UTC hello@padlet.com Problem Solving Task MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1769651055 . Existing cells in our body divides through the process of meiosis and mitosis to produce new cells. The division of the cells would slowly halve the size of the genome until each cell would die if there is no new copies of DNA is made before undergoes cell division process, which probably would not take long. Therefore, S phase of interphase in cell cycle of a cell is important in keeping the cells alive. What is the process involved in copying DNA in S phase? Explain the principles involved in the process. ]]> 2021-09-27 01:58:00 UTC https://padlet.com/MadamNash/Chap6_123/wish/1769651055 Problem Solving Task MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1769651858 Eukaryotic cells need to make proteins to carry out their day-to-day activities, like processing nutrients and growing. The cell’s DNA contains instructions for building these proteins but reading those instructions directly from DNA is cumbersome and could damage the DNA. Therefore, how would the cell transfer the instruction to make proteins? Explain the process that involved in the information transfer from DNA]]> 2021-09-27 01:58:21 UTC https://padlet.com/MadamNash/Chap6_123/wish/1769651858 Problem Solving Task MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1769652723 The cell in the small intestine had produced the temporary intermediate, mRNA molecule that carries the instructions to make a protein involved in the digestion process, digestive enzymes to break down food to provide nutrients and energy that our body needs. How does the process of making digestive enzyme in the cell in small intestines continue?  ]]> 2021-09-27 01:58:45 UTC https://padlet.com/MadamNash/Chap6_123/wish/1769652723 Problem Solving Task MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1769653621 . Assume that you have discovered two new strains of E.coli that has a mutation in the lac operon structures. One type of strain has mutation in operator region and another type in promoter region. Explain how this phenomenon would affect the metabolism of lactose.    ]]> 2021-09-27 01:59:08 UTC https://padlet.com/MadamNash/Chap6_123/wish/1769653621 6.4.4 and 6.4.5 rameshvasanth38 https://padlet.com/MadamNash/Chap6_123/wish/1770270316 In the absence and presence of lactose]]> 2021-09-27 07:02:00 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770270316 Enzymes involved in DNA replication are:Helicase (unwinds the DNA double helix)a protein known as helicase attaches to and breaks apart the hydrogen bonds between the bases on the DNA strands, thereby pulling apart the two strands.Gyrase (relieves the buildup of torque during unwinding)Primase (lays down RNA primers)DNA polymerase III (main DNA synthesis enzyme)DNA polymerase I (replaces RNA primers with DNA)Ligase (fills in the gaps) https://padlet.com/MadamNash/Chap6_123/wish/1770271084 2021-09-27 07:02:26 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770271084 DNA REPLICATION amirahkhalid7 https://padlet.com/MadamNash/Chap6_123/wish/1770274456
  • DNA replication the two old DNA strands serves as a template for the formation of an entire new strand. Because each of the two daughters of a dividing cell inherits a new DNA double helix containing one old and one new strand
  • DNA replication occurs in the cytoplasm of prokaryotes and in the nucleus of eukaryotes. 
  • S phase dna replication occur
  • the proposed models of DNA    replication.The conservative model.The semiconservative model.The dispersive model
  • Meselson and Stahl who proved   the correct model of  DNA replication
  • The experiment done by Meselson and Stahl demonstrated that DNA replicated semi-conservatively, meaning that each strand in a DNA molecule serves as a template for synthesis of a new, complementary strand


    • ]]>     2021-09-27 07:04:18 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770274456     Operon https://padlet.com/MadamNash/Chap6_123/wish/1770279544 The operon, defined in bacteria, is a group of contiguous genes which, on derepresssion, are transcribed into a single strand of messenger RNA. Both translation proceed from the operator end of the operon.

    Operons occur primarily in prokaryotes but also in some eukaryotes.
    Examples of prokaryotes are bacteria, archaea, and cyanobacteria (blue-green algae).

    The best-studied examples of operons are from the bacterium Escherichia coli (E. coli), and they involve the enzymes of lactose metabolism and tryptophan biosynthesis. Because the lactose (lac) operon shares many features with other operons, its organization and regulation are described in detail below.

    The operon model of prokaryotic gene regulation was proposed by the French microbiologist Fancois Jacob and Jacques Monodin early 1960s. Groups of genes coding for related proteins are arranged in units known as operons.

    Operons can be of two types:

    • Inducible – This type of operon is switched on in the presence of inducer, e.g. Lac operon
    • Repressible – It is usually present in anabolic pathways. The operon is active and the functional product or enzyme is present normally in the cell. When the end product reaches the maximum value, the operon is turned off. E.g. Trp operon
    ]]>     2021-09-27 07:06:52 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770279544     MECHANISM OF THE OPERON IN THE ABSENCE OF LACTOSE alinyusdi https://padlet.com/MadamNash/Chap6_123/wish/1770285677
    1) Repressor attaches itself to the operator and blocked part of promoter

    2) RNA polymerase cannot bind to the promoter.

    3) The operon is not active (TRANSCRIPTION IS BLOCKED BY REPRESSOR)

    4) 3 structural enzymes cannot be synthesized.(β-galactosidase, Permease, Transacetylase)

     

    ]]>     2021-09-27 07:09:56 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770285677     Why (+ important points) sharllynraaj https://padlet.com/MadamNash/Chap6_123/wish/1770287188
    Why Replicate DNA?

    DNA     is the genetic material that defines every cell. Before a cell duplicates and is divided into new daughter cells through either mitosis or meiosis, biomolecules and organelles must be copied to be distributed among the cells. DNA, found within the nucleus, must be replicated in order to ensure that each new cell receives the correct number of chromosomes. The process of DNA duplication is called DNA replication. Replication follows several steps that involve multiple proteins called replication enzymes and RNA. In eukaryotic cells, such as animal cells and plant cells, DNA replication occurs in the S phase of interphase during the cell cycle. The process of DNA replication is vital for cell growth, repair, and reproduction in organisms.

    Key Takeaways
    • Deoxyribonucleic acid, commonly known as DNA, is a nucleic acid that has three main components: a deoxyribose sugar, a phosphate, and a nitrogenous base.
    • Since DNA contains the genetic material for an organism, it is important that it be copied when a cell divides into daughter cells. The process that copies DNA is called replication.
    • Replication involves the production of identical helices of DNA from one double-stranded molecule of DNA.
    • Enzymes are vital to DNA replication since they catalyze very important steps in the process.
    • The overall DNA replication process is extremely important for both cell growth and reproduction in organisms. It is also vital in the cell repair process.
    ]]>     2021-09-27 07:10:36 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770287188     6.4.4 and 6.4.5 absence and presence of lactose rameshvasanth38 https://padlet.com/MadamNash/Chap6_123/wish/1770294111 2021-09-27 07:13:57 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770294111 LAC OPERON nurainamaziah_ https://padlet.com/MadamNash/Chap6_123/wish/1770294517 The lac operon is the section of DNA that acts as an on/off switch for genes that control the metabolism of lactose.

    Lactose is not a common sugar, so there is not a greet need for these enzymes.

    When lactose is present, lac operon is switched on and produces enzymes.


    ]]>     2021-09-27 07:14:09 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770294517     https://padlet.com/MadamNash/Chap6_123/wish/1770298684 2021-09-27 07:16:03 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770298684 In the presence of lactose rameshvasanth38 https://padlet.com/MadamNash/Chap6_123/wish/1770307465 2021-09-27 07:20:13 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770307465 Presence of lactose rameshvasanth38 https://padlet.com/MadamNash/Chap6_123/wish/1770309701 2021-09-27 07:21:15 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770309701 What happens if dna is not replicated properly sharllynraaj https://padlet.com/MadamNash/Chap6_123/wish/1770311946 Replicating DNA is fragile, and can break during the duplication process. In fact, broken chromosomes are often the source of DNA rearrangements and can change the genetic program of a cell. These changes can trigger a growth advantage in a single cell in your body, and when that cell continues to divide, tumors arise. Fortunately, our cells have defense mechanisms to shield us from these damaging events.]]> 2021-09-27 07:22:16 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770311946 Formation of new strand is from 5’ to 3’. mms2023177460 https://padlet.com/MadamNash/Chap6_123/wish/1770321896 DNA polymerases can only make DNA in the 5' to 3' direction. 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. At the end of the DNA replication, a double-stranded DNA molecule is copied to produce two identical DNA molecules.

    ]]>     2021-09-27 07:26:28 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770321896     DNA Replication Diagram mms2023177460 https://padlet.com/MadamNash/Chap6_123/wish/1770347782 • DNA is always synthesized in the 5'-to-3' direction, meaning that nucleotides are added only to the 3' end of the growing strand. As shown in Figure 1, the 5'-phosphate group of the new nucleotide binds to the 3'-OH group of the last nucleotide of the growing strand.
    • 3′ is pronounced ‘three prime’ and 5′ is pronounced ‘five prime
    • The primer acts as the starting point for DNA synthesis. DNA polymerase? binds to the leading strand and then 'walks' along it, adding new complementary? nucleotide?bases (A, C, G and T) to the strand of DNA in the 5' to 3' direction. This sort of replication is called continuous.
    • 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.
    • 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.

    Unidirectional and bidirectional DNA synthesis

    • Unidirectional DNA synthesis is only seen in a few prokaryotes whereas bidirectional DNA replication occurs in all eukaryotes and many prokaryotes.

    • The difference between unidirectional replication of DNA and bidirectional replication of DNA is as follows:

    UNIDIRECTIONAL | BIDIRECTIONAL
    In unidirectional synthesis, the replication process occurs in only one direction. | In bidirectional synthesis, the replication process occurs in two directions.
    In unidirectional replication only one replication fork is formed. | In bidirectional replication two replication forks are formed
    In unidirectional replication, only one end of the replication eye is moving or growing. | In bidirectional replication, both the ends are moving.




    ]]>     2021-09-27 07:39:11 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770347782     youtube video translation https://padlet.com/MadamNash/Chap6_123/wish/1770355382 2021-09-27 07:42:43 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770355382 PROMOTER, AN OPERATOR, THREE STRUCTURAL GENES nurainamaziah_ https://padlet.com/MadamNash/Chap6_123/wish/1770359202 The lac operon found in E.coli consists of a promoter, an operator, and three structural genes lacZ (S1), lacY (S2) and lacA (S3).

    *Promoter
    RNA polymerase binding site on DNA to initiate transcription.

    *Operator
    Switch thats control transcription of structural genes (on or off) by allowing or preventing RNA polymerase binding to promoter.

    *Structural Genes
    Code for three enzymes with specific functions.

    ]]>     2021-09-27 07:44:38 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770359202     semiconservative amirahkhalid7 https://padlet.com/MadamNash/Chap6_123/wish/1770397495 2021-09-27 08:04:38 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770397495 The complementary strand amirahkhalid7 https://padlet.com/MadamNash/Chap6_123/wish/1770412878 DNA consists of complementary polynucleotide strands. DNA in a double helix are anti-parallel, meaning that they are oriented in opposite directions to each other. The bases from opposite strands form complementary base pairing with each other.

    ]]>     2021-09-27 08:12:12 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770412878     B-galactosidase Structure nurainamaziah_ https://padlet.com/MadamNash/Chap6_123/wish/1770420536 Hydrolyses lactose to glucose and galactose]]> 2021-09-27 08:16:00 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770420536 Lactose Permease nurainamaziah_ https://padlet.com/MadamNash/Chap6_123/wish/1770440423 Membrane bound transport lactose into the cell.]]> 2021-09-27 08:26:30 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770440423 Transacetylase nurainamaziah_ https://padlet.com/MadamNash/Chap6_123/wish/1770456649 Transfer an acetly group from acetyl CoA to B-galactosidase]]> 2021-09-27 08:34:33 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770456649 GENE REGULATION https://padlet.com/MadamNash/Chap6_123/wish/1770478677 Gene regulation is the process of turning genes on and off.

    Why is important?
    • Help organism respond to its environment.
    • Ensures that the appropriate genes are expressed at the proper times.

    The on and off switch is a segment of DNA called operator.
    • Operator can be blocked by repressor.
    • If it binds with operator, it will block RNA polymerase(act as the off switch)
    • Why? To prevent the transcription of genes.🥸

    There is a gene on the operon that codes the producing of repressor
    • Eg. lacI








    ]]>     2021-09-27 08:45:27 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770478677     Regulatory Gene (lacI gene) nurainamaziah_ https://padlet.com/MadamNash/Chap6_123/wish/1770488221 Regulatory gene is located upstream of the lac operon and encodes for the synthesis of an active repressor.]]> 2021-09-27 08:50:17 UTC https://padlet.com/MadamNash/Chap6_123/wish/1770488221 The amino acids specified by each mRNA codon. Multiple codons can code for the same amino acid. https://padlet.com/MadamNash/Chap6_123/wish/1771211459 During translation(second major step in gene expression),
    ~The mRNA is "read" according to the genetic code,which relates the DNA sequence to the amino acid sequence in proteins.]]>     2021-09-27 13:55:56 UTC https://padlet.com/MadamNash/Chap6_123/wish/1771211459     sharllynraaj https://padlet.com/MadamNash/Chap6_123/wish/1771296996 Step 1: Replication Fork Formation
    Before DNA can be replicated, the double stranded molecule must be “unzipped” into two single strands. DNA has four bases called adenine (A), thymine (T), cytosine (C) and guanine (G) that form pairs between the two strands. Adenine only pairs with thymine and cytosine only binds with guanine. In order to unwind DNA, these interactions between base pairs must be broken. This is performed by an enzyme known as DNA helicase. DNA helicase disrupts the hydrogen bonding between base pairs to separate the strands into a Y shape known as the replication fork. This area will be the template for replication to begin.
    DNA is directional in both strands, signified by a 5' and 3' end. This notation signifies which side group is attached the DNA backbone. The 5' end has a phosphate (P) group attached, while the 3' end has a hydroxyl (OH) group attached. This directionality is important for replication as it only progresses in the 5' to 3' direction. However, the replication fork is bi-directional; one strand is oriented in the 3' to 5' direction (leading strand) while the other is oriented 5' to 3' (lagging strand). The two sides are therefore replicated with two different processes to accommodate the directional difference.Replication Begins Step 2: Primer Binding
    The leading strand is the simplest to replicate. Once the DNA strands have been separated, a short piece of RNA called a primer binds to the 3' end of the strand. The primer always binds as the starting point for replication. Primers are generated by the enzyme DNA primase.
    DNA Replication: Elongation

     DNA polymerases (blue) attach themselves to the DNA and elongate the new strands by adding nucleotide bases.
    UIG / Getty Images
    Step 3: Elongation

    Enzymes known as DNA polymerases are responsible creating the new strand by a process called elongation. There are five different known types of DNA polymerases in bacteria and human cells. In bacteria such as E. coli, polymerase III is the main replication enzyme, while polymerase I, II, IV and V are responsible for error checking and repair. DNA polymerase III binds to the strand at the site of the primer and begins adding new base pairs complementary to the strand during replication. In eukaryotic cells, polymerases alpha, delta, and epsilon are the primary polymerases involved in DNA replication. Because replication proceeds in the 5' to 3' direction on the leading strand, the newly formed strand is continuous.


    The lagging strand begins replication by binding with multiple primers. Each primer is only several bases apart. DNA polymerase then adds pieces of DNA, called Okazaki fragments, to the strand between primers. This process of replication is discontinuous as the newly created fragments are disjointed.

    Step 4: Termination

    Once both the continuous and discontinuous strands are formed, an enzyme called exonuclease removes all RNA primers from the original strands. These primers are then replaced with appropriate bases. Another exonuclease “proofreads” the newly formed DNA to check, remove and replace any errors. Another enzyme called DNA ligase joins Okazaki fragments together forming a single unified strand. The ends of the linear DNA present a problem as DNA polymerase can only add nucleotides in the 5′ to 3′ direction. The ends of the parent strands consist of repeated DNA sequences called telomeres. Telomeres act as protective caps at the end of chromosomes to prevent nearby chromosomes from fusing. A special type of DNA polymerase enzyme called telomerase catalyzes the synthesis of telomere sequences at the ends of the DNA. Once completed, the parent strand and its complementary DNA strand coils into the familiar double helix shape. In the end, replication produces two DNA molecules, each with one strand from the parent molecule and one new strand.

    Replication Enzymes

     DNA polymerase molecule.
    Cultura / Getty Images

    DNA replication would not occur without enzymes that catalyze various steps in the process. Enzymes that participate in the eukaryotic DNA replication process include:

    • DNA helicase - unwinds and separates double stranded DNA as it moves along the DNA. It forms the replication fork by breaking hydrogen bonds between nucleotide pairs in DNA.
    • DNA primase - a type of RNA polymerase that generates RNA primers. Primers are short RNA molecules that act as templates for the starting point of DNA replication.
    • DNA polymerases - synthesize new DNA molecules by adding nucleotides to leading and lagging DNA strands.
    • Topoisomerase or DNA Gyrase - unwinds and rewinds DNA strands to prevent the DNA from becoming tangled or supercoiled.
    • Exonucleases - group of enzymes that remove nucleotide bases from the end of a DNA chain.
    • DNA ligase - joins DNA fragments together by forming phosphodiester bonds between nucleotides.
    DNA Replication Summary

     Replication of DNA.
    Francis Leroy / Getty Images

    DNA replication is the production of identical DNA helices from a single double-stranded DNA molecule. Each molecule consists of a strand from the original molecule and a newly formed strand. Prior to replication, the DNA uncoils and strands separate. A replication fork is formed which serves as a template for replication. Primers bind to the DNA and DNA polymerases add new nucleotide sequences in the 5′ to 3′ direction.


    This addition is continuous in the leading strand and fragmented in the lagging strand. Once elongation of the DNA strands is complete, the strands are checked for errors, repairs are made, and telomere sequences are added to the ends of the DNA.



    ]]>     2021-09-27 14:17:59 UTC https://padlet.com/MadamNash/Chap6_123/wish/1771296996     LACTOSE nurainamaziah_ https://padlet.com/MadamNash/Chap6_123/wish/1773374121
    OTHER NAMES:
    D-lactose; milk sugar; many others

    FORMULA:
    C12H22O11

    ELEMENTS:
    Carbon, hydrogen, oxygen

    COMPOUND TYPE:
    Disaccharide; carbohydrate (organic)

    STATE:
    Solid

    MOLECULAR WEIGHT:
    342.30 g/mol

    ]]>     2021-09-28 04:44:22 UTC https://padlet.com/MadamNash/Chap6_123/wish/1773374121     https://padlet.com/MadamNash/Chap6_123/wish/1774028198 Transcription: control from the promoter and termination sequence
    The 

    promoter’s role is to selectively turn on the ALS 
    gene in cells that will need the ALS enzyme. The promoter accomplishes this by its specific nucleotide sequences. We will discuss the regulation of gene expression in more detail later. What cells in a plant will need the ALS 
    enzyme? All cells that are making 
    proteins. Obviously this will be all cells in the plant at some stage of development. Therefore the ALS 
    gene
     has a promoter sequence that allows the gene to be turned on in all types of cells.
    When the ALS gene is turned on, transcription can take place. Like most chemistry in the cell, enzymes will be needed for 

    gene expression.
     
    RNA polymerase
     is the 
    transcription
     enzyme (Fig. 9) which will bind to the DNA sequences in the ALS promoter and interact with one strand of the gene (the coding strand).

    Figure 9a. The promoter has DNA sequences that signal the cell when to turn on the gene and where to start reading the gene information. (image by d. Namuth-Covert)


    Figure 9b. RNA Polymerase binds to the promoter to initiate transcription. (Image by D. Namuth-Covert)

    RNA polymerase can literally move along the gene promoter until it encounters a series of A and T nucleotides called the TATA box (Fig 10.). The TATA box signals RNA polymerase that it has reached the end of the promoter. Now the enzyme has the “green light” to read the coding strand 

    DNA
     and make RNA. The procedure works much like DNA replication. RNA polymerase will read the DNA in a 3’ to 5’ direction and build the RNA 5’ to 3’. Unlike DNA replication though, only one DNA strand is read and the transcription process must end once the RNA polymerase reaches the end of the ALS gene. If RNA polymerase kept going along that strand of the DNA making up the chromosome, other genes that are on the same 
    chromosome
     might be expressed in the wrong cells or wrong times.

    Figure 10. RNA polymerase encounters the TATA box at the end of the promoter. This signals where to begin the reading of the coding region. (Image by D. Namuth-Covert)

    How is the RNA polymerase signaled that it has reached the end of the gene? That is the role of a 

    termination sequence
     in the gene (Fig. 11). The termination sequences signal the end of the gene and can work in a number of ways. One transcription termination strategy will be described here.The 
    nucleotides
     that make up the termination sequence of the ALS gene could be ordered to form a palindrome. This means that the nucleotides being placed in the RNA can fold back on themselves and form a hairpin loop (Figs. 12-14)

    Figure 11. When RNA polymerase reads the termination sequence it is signaled to quit reading the gene’s coding strand. (Image by D. Namuth-Covert)


    Figure 12. RNA polymerase has just finished reading the coding region and is starting to read the termination sequence. (dashes are unspecified nucleotides). (Image by D. Namuth Covert)


    Figure 13. The termination sequence is palindromic. The RNA being made has a sequence that can form a hairpin loop. (Image by D. Lee)


    Figure 14. Formation of the hairpin in the newly made RNA disrupts the RNA polymerase, halting transcription. (Image by D. Lee)

    While no geneticist has actually viewed this hairpin loop formation in action, it is believed that the hairpin formation snaps the RNA polymerase off the DNA coding strand and releases the RNA message. Transcription of an RNA that has the 

    coding region
     information is now completed. Each time an RNA polymerase goes through the process, one copy of the RNA is made by reading the DNA template.The type of RNA made from transcription of the ALS gene is called a messenger RNA or mRNA for short. Some 
    genes
     can encode transfer RNA (tRNA) or ribosomal RNA (rRNA). These RNA molecules have special roles in the next part of gene expression called translation. Once an 
    mRNA
     is transcribed some modifications will occur in the nucleus. We will describe some of the post-transcriptional processes later. For now lets follow the ALS mRNA onto the 
    translation
     step of gene expression.

    ]]>     2021-09-28 09:29:07 UTC https://padlet.com/MadamNash/Chap6_123/wish/1774028198     https://padlet.com/MadamNash/Chap6_123/wish/1774032125 2021-09-28 09:31:13 UTC https://padlet.com/MadamNash/Chap6_123/wish/1774032125 https://padlet.com/MadamNash/Chap6_123/wish/1774038779
    Transcription overview

    Transcription is the first step of gene expression. During this process, the DNA sequence of a gene is copied into RNA.
    Before transcription can take place, the DNA double helix must unwind near the gene that is getting transcribed. The region of opened-up DNA is called a transcription bubble.
    In transcription, a region of DNA opens up. One strand, the template strand, serves as a template for synthesis of a complementary RNA transcript. The other strand, the coding strand, is identical to the RNA transcript in sequence, except that it has uracil (U) bases in place of thymine (T) bases.
    Example:
    Coding strand: 5'-ATGATCTCGTAA-3' Template strand: 3'-TACTAGAGCATT-5' RNA transcript: 5'-AUGAUCUCGUAA-3'
    In translation, the RNA transcript is read to produce a polypeptide.
    Example:
    RNA transcript: 5'-AUG AUC UCG UAA-3' Polypeptide: (N-terminus) Met - Ile - Ser - [STOP] (C-terminus)
    Transcription uses one of the two exposed DNA strands as a template; this strand is called the template strand. The RNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate (or coding) strand. However, there is one important difference: in the newly made RNA, all of the T nucleotides are replaced with U nucleotides.
    The site on the DNA from which the first RNA nucleotide is transcribed is called the
    +1+1
    plus, 1 site, or the initiation site. Nucleotides that come before the initiation site are given negative numbers and said to be upstream. Nucleotides that come after the initiation site are marked with positive numbers and said to be downstream.
    If the gene that's transcribed encodes a protein (which many genes do), the RNA molecule will be read to make a protein in a process called translation.
    [Are there steps between transcription and translation?]

    RNA polymerase

    RNA polymerases are enzymes that transcribe DNA into RNA. Using a DNA template, RNA polymerase builds a new RNA molecule through base pairing. For instance, if there is a G in the DNA template, RNA polymerase will add a C to the new, growing RNA strand.
    RNA polymerase synthesizes an RNA strand complementary to a template DNA strand. It synthesizes the RNA strand in the 5' to 3' direction, while reading the template DNA strand in the 3' to 5' direction. The template DNA strand and RNA strand are antiparallel.
    RNA transcript: 5'-UGGUAGU...-3' (dots indicate where nucleotides are still being added at 3' end) DNA template: 3'-ACCATCAGTC-5'
    RNA polymerase always builds a new RNA strand in the 5’ to 3’ direction. That is, it can only add RNA nucleotides (A, U, C, or G) to the 3' end of the strand.
    [What do 5' and 3' mean?]
    RNA polymerases are large enzymes with multiple subunits, even in simple organisms like bacteria. Humans and other eukaryotes have three different kinds of RNA polymerase: I, II, and III. Each one specializes in transcribing certain classes of genes. Plants have an additional two kinds of RNA polymerase, IV and V, which are involved in the synthesis of certain small RNAs.

    Transcription initiation

    To begin transcribing a gene, RNA polymerase binds to the DNA of the gene at a region called the promoter. Basically, the promoter tells the polymerase where to "sit down" on the DNA and begin transcribing.
    The promoter region comes before (and slightly overlaps with) the transcribed region whose transcription it specifies. It contains recognition sites for RNA polymerase or its helper proteins to bind to. The DNA opens up in the promoter region so that RNA polymerase can begin transcription.
    Each gene (or, in bacteria, each group of genes transcribed together) has its own promoter. A promoter contains DNA sequences that let RNA polymerase or its helper proteins attach to the DNA. Once the transcription bubble has formed, the polymerase can start transcribing.

    Promoters in bacteria

    To get a better sense of how a promoter works, let's look an example from bacteria. A typical bacterial promoter contains two important DNA sequences, the
    -
    1010
    10 and
    -
    3535
    35 elements.
    RNA polymerase recognizes and binds directly to these sequences. The sequences position the polymerase in the right spot to start transcribing a target gene, and they also make sure it's pointing in the right direction.
    [How?]
    Once the RNA polymerase has bound, it can open up the DNA and get to work. DNA opening occurs at the
    -
    1010
    10 element, where the strands are easy to separate due to the many As and Ts (which bind to each other using just two hydrogen bonds, rather than the three hydrogen bonds of Gs and Cs).
    Bacterial promoter. The promoter lies at the start of the transcribed region, encompassing the DNA before it and slightly overlapping with the transcriptional start site. The promoter contains two elements, the -35 element and the -10 element. The -35 element is centered about 35 nucleotides upstream of (before) the transcriptional start site (+1), while the -10 element is centered about 10 nucleotides before the transcriptional start site. In this particular example, the sequence of the -35 element (on the coding strand) is 5'-TTGACG-3', while the sequence of the -10 element (on the coding strand) is 5'-TATAAT-3'. The RNA polymerase has regions that specifically bind to the -10 and -35 elements.
    The 
    -
    1010
    10 and the 
    -
    3535
    35 elements get their names because they come 
    3535
    35 and 
    1010
    10 nucleotides before the initiation site (
    +1+1
    plus, 1 in the DNA). The minus signs just mean that they are before, not after, the initiation site.

    Promoters in humans

    In eukaryotes like humans, the main RNA polymerase in your cells does not attach directly to promoters like bacterial RNA polymerase. Instead, helper proteins called basal (general) transcription factors bind to the promoter first, helping the RNA polymerase in your cells get a foothold on the DNA.
    Many eukaryotic promoters have a sequence called a TATA box. The TATA box plays a role much like that of the
    -
    1010
    10 element in bacteria. It's recognized by one of the general transcription factors, allowing other transcription factors and eventually RNA polymerase to bind. It also contains lots of As and Ts, which make it easy to pull the strands of DNA apart.
    The promoter of a eukaryotic gene is shown. The promoter lies upstream of and slightly overlaps with the transcriptional start site (+1). It contains a TATA box, which has a sequence (on the coding strand) of 5'-TATAAA-3'. The first eukaryotic general transcription factor binds to the TATA box. Then, other general transcription factors bind. Finally, RNA polymerase II and some additional transcription factors bind to the promoter.

    Elongation

    Once RNA polymerase is in position at the promoter, the next step of transcription—elongation—can begin. Basically, elongation is the stage when the RNA strand gets longer, thanks to the addition of new nucleotides.
    During elongation, RNA polymerase "walks" along one strand of DNA, known as the template strand, in the 3' to 5' direction. For each nucleotide in the template, RNA polymerase adds a matching (complementary) RNA nucleotide to the 3' end of the RNA strand.
    [See the chemical reaction]
    RNA polymerase synthesizes an RNA transcript complementary to the DNA template strand in the 5' to 3' direction. It moves forward along the template strand in the 3' to 5' direction, opening the DNA double helix as it goes. The synthesized RNA only remains bound to the template strand for a short while, then exits the polymerase as a dangling string, allowing the DNA to close back up and form a double helix.
    In this example, the sequences of the coding strand, template strand, and RNA transcript are:
    Coding strand: 5' - ATGATCTCGTAA-3'
    Template strand: 3'-TACTAGAGCATT-5'
    RNA: 5'-AUGAUC...-3' (the dots indicate where nucleotides are still being added to the RNA strand at its 3' end)
    The RNA transcript is nearly identical to the non-template, or coding, strand of DNA. However, RNA strands have the base uracil (U) in place of thymine (T), as well as a slightly different sugar in the nucleotide. So, as we can see in the diagram above, each T of the coding strand is replaced with a U in the RNA transcript.
    [See a diagram of the bases]
    The picture below shows DNA being transcribed by many RNA polymerases at the same time, each with an RNA "tail" trailing behind it. The polymerases near the start of the gene have short RNA tails, which get longer and longer as the polymerase transcribes more of the gene.
    In the microscope image shown here, a gene is being transcribed by many RNA polymerases at once. The RNA chains are shortest near the beginning of the gene, and they become longer as the polymerases move towards the end of the gene. This pattern creates a kind of wedge-shaped structure made by the RNA transcripts fanning out from the DNA of the gene.
    _Image modified from "Transcription label en," by Dr. Hans-Heinrich Trepte (CC BY-SA 3.0). The modified image is licensed under a CC BY-SA 3.0 license._

    Transcription termination

    RNA polymerase will keep transcribing until it gets signals to stop. The process of ending transcription is called termination, and it happens once the polymerase transcribes a sequence of DNA known as a terminator.

    Termination in bacteria

    There are two major termination strategies found in bacteria: Rho-dependent and Rho-independent.
    In Rho-dependent termination, the RNA contains a binding site for a protein called Rho factor. Rho factor binds to this sequence and starts "climbing" up the transcript towards RNA polymerase.
    Rho-dependent termination. The terminator is a region of DNA that includes the sequence that codes for the Rho binding site in the mRNA, as well as the actual transcription stop point (which is a sequence that causes the RNA polymerase to pause so that Rho can catch up to it). Rho binds to the Rho binding site in the mRNA and climbs up the RNA transcript, in the 5' to 3' direction, towards the transcription bubble where the polymerase is. When it catches up to the polymerase, it will cause the transcript to be released, ending transcription.
    When it catches up with the polymerase at the transcription bubble, Rho pulls the RNA transcript and the template DNA strand apart, releasing the RNA molecule and ending transcription. Another sequence found later in the DNA, called the transcription stop point, causes RNA polymerase to pause and thus helps Rho catch up.
    ^4
    4
    start superscript, 4, end superscript
    Rho-independent termination depends on specific sequences in the DNA template strand. As the RNA polymerase approaches the end of the gene being transcribed, it hits a region rich in C and G nucleotides. The RNA transcribed from this region folds back on itself, and the complementary C and G nucleotides bind together. The result is a stable hairpin that causes the polymerase to stall.
    Rho-independent termination. The terminator DNA sequence encodes a region of RNA that folds back on itself to form a hairpin. The hairpin is followed by a series of U nucleotides in the RNA (not pictured). The hairpin causes the polymerase to stall, and the weak base pairing between the A nucleotides of the DNA template and the U nucleotides of the RNA transcript allows the transcript to separate from the template, ending transcription.
    In a terminator, the hairpin is followed by a stretch of U nucleotides in the RNA, which match up with A nucleotides in the template DNA. The complementary U-A region of the RNA transcript forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase, produces enough instability for the enzyme to fall off and liberate the new RNA transcript.
    [Transcription termination in eukaryotes]

    What happens to the RNA transcript?

    After termination, transcription is finished. An RNA transcript that is ready to be used in translation is called a messenger RNA (mRNA). In bacteria, RNA transcripts are ready to be translated right after transcription. In fact, they're actually ready a little sooner than that: translation may start while transcription is still going on!
    In the diagram below, mRNAs are being transcribed from several different genes. Although transcription is still in progress, ribosomes have attached each mRNA and begun to translate it into protein. When an mRNA is being translated by multiple ribosomes, the mRNA and ribosomes together are said to form a polyribosome.
    Illustration shows mRNAs being transcribed off of genes. Ribosomes attach to the mRNAs before transcription is done and begin making protein.
    Image modified from "Prokaryotic transcription: Figure 3, by OpenStax College, Biology, CC BY 4.0.
    Why can transcription and translation happen simultaneously for an mRNA in bacteria? One reason is that these processes occur in the same 5' to 3' direction. That means one can follow or "chase" another that's still occurring. Also, in bacteria, there are no internal membrane compartments to separate transcription from translation.
    The picture is different in the cells of humans and other eukaryotes. That's because transcription happens in the nucleus of human cells, while translation happens in the cytosol. Also, in eukaryotes, RNA molecules need to go through special processing steps before translation. That means translation can't start until transcription and RNA processing are fully finished. You can learn more about these steps in the transcription and RNA processing video
    ]]>     2021-09-28 09:34:34 UTC https://padlet.com/MadamNash/Chap6_123/wish/1774038779     Journal research MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1774194666 2021-09-28 10:57:31 UTC https://padlet.com/MadamNash/Chap6_123/wish/1774194666 Vaksin mRNA for Covid -19 MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1774209796 2021-09-28 11:06:15 UTC https://padlet.com/MadamNash/Chap6_123/wish/1774209796 MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1774210873 2021-09-28 11:06:55 UTC https://padlet.com/MadamNash/Chap6_123/wish/1774210873 MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1774222822 2021-09-28 11:13:38 UTC https://padlet.com/MadamNash/Chap6_123/wish/1774222822 MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1774226456 2021-09-28 11:15:30 UTC https://padlet.com/MadamNash/Chap6_123/wish/1774226456 MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1774230031 2021-09-28 11:17:29 UTC https://padlet.com/MadamNash/Chap6_123/wish/1774230031 MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1774251553 2021-09-28 11:28:54 UTC https://padlet.com/MadamNash/Chap6_123/wish/1774251553 MadamNash https://padlet.com/MadamNash/Chap6_123/wish/1774265353 2021-09-28 11:36:01 UTC https://padlet.com/MadamNash/Chap6_123/wish/1774265353 mms2023177460 https://padlet.com/MadamNash/Chap6_123/wish/1785558072 Note: 
    - DNA replication starts at a point or DNA sequence known as origin of replication. DNA replication occurs in cytoplasm in prokaryotes and it occurs in nucleus of eukaryotes but the basic process of the replication remains same in both eukaryotes as well as prokaryotes. 
    - Although DNA synthesis occurs in different directions in different organisms, the DNA polymerase acts in the same direction ie.5'-3' only.]]>     2021-10-02 06:32:35 UTC https://padlet.com/MadamNash/Chap6_123/wish/1785558072     rahidatulhani https://padlet.com/MadamNash/Chap6_123/wish/1786124853 2021-10-02 16:31:34 UTC https://padlet.com/MadamNash/Chap6_123/wish/1786124853 rahidatulhani https://padlet.com/MadamNash/Chap6_123/wish/1786126564 2021-10-02 16:32:52 UTC https://padlet.com/MadamNash/Chap6_123/wish/1786126564 rahidatulhani https://padlet.com/MadamNash/Chap6_123/wish/1786127989 2021-10-02 16:34:09 UTC https://padlet.com/MadamNash/Chap6_123/wish/1786127989 https://padlet.com/MadamNash/Chap6_123/wish/1787248092 2021-10-03 13:22:13 UTC https://padlet.com/MadamNash/Chap6_123/wish/1787248092 https://padlet.com/MadamNash/Chap6_123/wish/1787256161 2021-10-03 13:27:02 UTC https://padlet.com/MadamNash/Chap6_123/wish/1787256161 https://padlet.com/MadamNash/Chap6_123/wish/1788718469 2021-10-04 06:42:15 UTC https://padlet.com/MadamNash/Chap6_123/wish/1788718469 https://padlet.com/MadamNash/Chap6_123/wish/1788803861 2021-10-04 07:29:06 UTC https://padlet.com/MadamNash/Chap6_123/wish/1788803861 power point presentation mms2123133003 https://padlet.com/MadamNash/Chap6_123/wish/1791746527 2021-10-05 04:19:39 UTC https://padlet.com/MadamNash/Chap6_123/wish/1791746527 ASSIGNMENT GROUP 4 nurainamaziah_ https://padlet.com/MadamNash/Chap6_123/wish/1795607140 2021-10-06 06:59:40 UTC https://padlet.com/MadamNash/Chap6_123/wish/1795607140