DNA Expression 12th Grade PDF

DNA 12th grade EXPRESSION Protein Synthesis Transcription & Translation LET’S QUICKLY REVIEW DNA Replication 1) Given the DNA sequence 5’-CCTAGAA-3’, the complementary strand would read… a) 3’ GGATCTT 5’ b) 3’ AAGATCC...

DNA 12th grade EXPRESSION Protein Synthesis Transcription & Translation LET’S QUICKLY REVIEW DNA Replication 1) Given the DNA sequence 5’-CCTAGAA-3’, the complementary strand would read… a) 3’ GGATCTT 5’ b) 3’ AAGATCC 5’ c) 5’ GGTATTC 3’ d) 5’ GGATCTT 3’ LET’S QUICKLY REVIEW DNA Replication 2) The leading strand of a DNA molecule has the following sequence: 5’-CGCATGTAGCGA-3’ What is the complementary (parent) strand to the leading strand shown above? 3’-GCGTACATCGCT-5’ LET’S QUICKLY REVIEW DNA Replication 2) The leading strand of a DNA molecule has the following sequence: 5’-CGCATGTAGCGA-3’ If this is the leading strand sequence, what would the lagging strand sequence be? 3’-GCGTACATCGCT-5’  3’ 5’ 5’ 3’ Replication Fork H The Leading and 5’ Lagging Strands 3’ are 3’ Complementary! 5’  THINK PAIR SHARE Step 1: For 5 minutes, individually think about what you think Transcription is. Step 2: Pair-up (or groups of 3) and discuss your thoughts. Come up with a final definition or explanation. Step 3: Share your group’s definition/explanation with the class! 01 CENTRAL DOGMA The Flow of Genetic Information  WHY DO CELLS MAKE PROTEIN Muscular Contraction Hormones Ex. Insulin Protection Ex. Myosin and Ex. Immunoglobulin (antibody) Actin Receptor Structure Ex. Keratin Ex. Rhodopsin Transport Ex. Hemoglobin Storage Enzyme Ex. Ferritin Ex. Rubisco  02 TRANSCRIPTION Let’s start talking about the steps involved in Gene Expression. Transcription In order to synthesize protein, DNA must be converted to RNA first. Why can’t protein be synthesized directly from DNA? DNA must converted to another form of nucleic acid (RNA) in order to be “read” by the machinery that creates the proteins (polypeptides). Transcription: mechanism by which the information coded in nucleic acids of DNA is copied into the nucleic acids of RNA; something rewritten in the same language.  Transcription Differences Eukaryotes Prokaryotes DNA (Deoxyribonucleic Acid) RNA (Ribonucleic Acid) Double Stranded Single Stranded Adenine pairs with Thymine Adenine pairs with Uracil Deoxyribose sugar Ribose Sugar Transcription - Initiation The enzyme, RNA Polymerase, binds to the DNA and unwinds it near the beginning of the target gene. RNA Polymerase binds to a promoter. Promoter: a nucleotide sequence that lies just before a gene (~25 nucleotides) and allows for the binding of RNA polymerase. Eukaryotes: TATA Box Prokaryotes: TATAAT sequence Why do the promoters only have A & T base-pairs? A-T only has 2 H-Bonds, allowing RNA polymerase to use less energy to break the bonds in order to open up the DNA. Transcription - Elongation After binding to the promoter and opening up the DNA double helix, RNA polymerase begins to build the RNA molecule. RNA polymerase does not need a primer. RNA is made in the 5’→3’ direction, using the 3’ →5’ DNA strand as a template strand. Therefore, the beginning of the RNA strand is the 5’ end, and the other end is the 3’ end. As RNA polymerase moves along the DNA, it unwinds the DNA at the forward end of the enzyme. The new RNA molecule elongates as nucleotides are added, one by one. Transcription - Elongation Coding Strand: the DNA strand that is not being copied but contains the same sequence as the new RNA molecule Sense strand Coding strand Antisense strand Non-coding strand  Transcription - Elongation When the new RNA molecule is formed, it temporarily winds with the template DNA strand into a hybrid RNA–DNA double helix. Beyond this short region of pairing, the growing RNA strand unwinds from the DNA and extends from the RNA polymerase as a single nucleotide chain. As the RNA polymerase passes, the DNA double helix reforms. Multiple RNA polymerases can attach to a single DNA strand if the promoter region is available. Each polymerase would then make a RNA transcript.  Transcription - Elongation thousands When cells require a particular protein, they usually need to produce _______________ or millions even _______________ of copies. 375 million hemoglobin molecules. For example, a single red blood cell contains _____________ The process of making hemoglobin would be very slow if the gene had only one RNA polymerase enzyme making one mRNA molecule at a time. Many copies of mRNA are made so that many ribosomes can mass-produce the protein required. Transcription - Termination The transcription of a protein-coding gene is terminated when RNA polymerase recognizes a termination sequence. In prokaryotes, one termination mechanism involves a protein binding to the mRNA and stopping transcription. Termination sequence: a sequence of bases at the end of a gene that signals the RNA polymerase to stop transcribing  Different Types of RNA Messenger RNA (mRNA) varies in length, depending on the gene that has been copied acts as the intermediary between DNA and the Created by ribosomes RNA is translated into protein by ribosomes Polymerase II is the RNA version of the gene encoded by DNA Transfer RNA (tRNA) functions as the delivery system of amino acids to ribosomes as they synthesize proteins is very short, only 70 to 90 base pairs long Important for Translation Ribosomal RNA (rRNA) binds with proteins to form the ribosomes varies in length What is processing? Post-Transcriptional Modifications Newly synthesized pre-mRNA is not ready to leave the nucleus in order to reach the ribosomes (site of translation). Modifications include: 3’ poly(A) tail: a chain of adenine nucleotides that are added to the 39 end of the pre-mRNA molecule to protect it from enzymes in the cytosol 5’ cap (5’ G-cap): a sequence of seven Gs that is added to the start of a pre-mRNA molecule; ribosomes recognize this site and use it as the site of initial attachment Exon: a sequence of DNA or RNA that codes for part of a gene Intron: a non-coding sequence of DNA or RNA Small ribonucleoprotein (snRNP): a protein that binds to introns and signals them for removal Spliceosome: an enzyme-protein complex that removes introns from the mRNA Alternative Splicing Exons may be joined in different combinations to produce different mRNAs from a single DNA gene sequence. Alternative splicing: a process that produces different mRNAs from pre-mRNA (exons and introns), allowing more than one possible polypeptide to be made from a single gene. Around ¾ of human pre-mRNAs are subject to alternative splicing. Alternative splicing explains how humans only have 20,000 genes that can produce around 100,000 proteins. Transcription: Prokaryotes vs Eukaryotes  Exit Ticket Continue on with your worksheet! Don’t forget to bring it tomorrow!  Any Questions about the Worksheet? If you’re confused, feel free to ask any questions! If you didn’t get one, please let me know!  03 TRANSLATION Going from mRNA to Proteins What is needed for Translation? tRNA Ribosomes Small RNAs, around Translate mRNA into chains of amino 70-90 nucleotides long acids. (mRNAs are usually 2 Parts: Large and Small ribosomal hundreds of subunits. nucleotides long). Each subunit is made of rRNA and tRNAs have regions ribosomal proteins that base pair with themselves, leading to the cloverleaf pattern (4 double helical segments). At the tip of of one of the segments is an anticodon. tRNA Definitions Anticodon: the complementary sequence of base pairs on a tRNA that corresponds to a codon on an mRNA Codon: Three consecutive nucleotides in a DNA or RNA strand that correlate to a specific amino acid. Ex: a tRNA that is linked to serine (Ser) pairs 5’- A G U -3’ with the codon 5’-AGU-3’ in mRNA. The anticodon of the tRNA that pairs with this codon is 3’-UCA-5’. Each tRNA is specific to an amino acid. THE WOBBLE HYPOTHESIS The wobble hypothesis: Even though the third nucleotide in the mRNA differs (UAU and UAC), the same tRNA with the anticodon AUA will deliver tyrosine to the growing polypeptide chain. Therefore, fewer types of tRNA are required to deliver the 20 amino acids, even though 61 codons exist in the genetic code. Further Definitions Aminoacylation: the process by which a tRNA molecule is bound to its corresponding amino acid Aminoacyl-tRNA: a molecule of transfer RNA bound to its associated amino acid  Ribosome Structure A tRNA molecule, with an amino acid bound it, enters the ribosome on the right (A site). The anticodon on the tRNA pairs with the codon in the mRNA. Its amino acid will then be added to the growing polypeptide, which is currently attached to the tRNA in the middle of the ribosome (P site). Codon Chart Amino Acids The basic structure of the amino acid monomers is polar due to the N – H and O – H bonds. This polarity level changes depending on the 20 different side chains. TRANSLATION STEPS Initiating Translation Translation begins when the large and small ribosomal subunits interact with an mRNA molecule and the first aminoacyl-tRNA binds to the AUG start codon. The aminoacyl–tRNA that is used for initiation is a specialized initiator tRNA, which has an anticodon to the methionine-specifying AUG start codon. In Step 1 of the initiation process, the initiator methionine–tRNA (met–tRNA) forms a complex with the small ribosomal subunit.  Initiating Translation The complex binds to the mRNA at the 5’ cap and then moves along the mRNA (a process called scanning) until it reaches the first AUG codon. This is the start codon, and it is recognized by the anticodon of the Met–tRNA. Initiating Translation The large ribosomal subunit then binds to complete the ribosome. At the end of initiation, the initiator Met–tRNA is in the P site. After the initiator tRNA pairs with the AUG start codon, the subsequent stages of translation simply read the mRNA nucleotide bases, three at a time. A correct initiator tRNA–AUG pairing establishes the correct reading frame: the series of codons for the polypeptide that is encoded by the mRNA. Elongating the Polypeptide Chain 4 steps of the Elongation stage: 1. Met-tRNA (initiator tRNA) is bound to the P site. The A site is empty. 2. The second tRNA, with an appropriate anticodon and amino acid (AA2), binds to the codon in the A site of the ribosome. A GTP provides free energy for this step. Next, the amino acid (Met) is cleaved from the tRNA in the P site and forms a peptide bond with the amino acid (AA2) on the tRNA in the A site. This bond formation is catalyzed by peptidyl transferase, which is a ribosomal enzyme. The new polypeptide chain is attached to the tRNA in the A site and an empty tRNA remains at the P site. Elongating the Polypeptide Chain 4 steps of the Elongation stage: 3. The ribosome moves along the mRNA to the next codon. The two tRNAs remain bound to their respective codons, so this step positions the newly formed peptidyl–tRNA in the P site and generates a vacant A site. An appropriate tRNA moves into the A site, and Steps 2 and 3 are repeated. After each repeat, the empty tRNA that was in the P site moves to the E site. 4. The empty tRNA is released from the ribosome from the E site.  Termination of Protein Synthesis Begins when the A site of a ribosome arrives at a stop codon. When a stop codon appears, a protein release factor binds instead of an aminoacyl-tRNA. Thus, the polypeptide chain is released from the tRNA at the P site. As this occurs, the ribosomal subunit separate from the mRNA. STOP Codons: UAA - U Are Annoying UGA - U Go Away UAG - U Are Gone DNA MUTATIONS 04 What can change our DNA and our Proteins?  MUTATIONS Mutation: is a permanent change in the nucleotide sequence of a cell’s DNA Chromosomal mutations are large-scale mutations that may affect multiple genes ○ Ex: deletions, duplications, inversions, translocation Single-gene mutations are often point mutations that may affect the function of a gene, resulting in a loss-of-function or gain-of-function ○ Ex. substitution, insertion, or deletion of a single base pair Mutagens: are events or substances that increase the rate of changes to the DNA sequence of an organism’s genome. Ex. transposons, chemicals, radiations Type of Mutation Effect in Protein Expression reading frame for translation is altered due to insertion or frameshift mutation deletion of 1-2 base pairs new codon specifies same amino acid as old codon (i.e. silent mutation multiple ‘triplet codes’ code for one amino acid) missense mutation new codon specifies different amino acid than old codon a codon is changed to an early stop codon resulting in a nonsense mutation loss-of-function Prokaryotes vs Eukaryotes Translation Protein Challenge Click here for slides Each group has been given a Protein strand (do not write on this slip!) With your group, determine the associated mRNA strand and original DNA strand. Post your 3 strands on the Google Slides (find your group # and class section) Translation Worksheet Make a copy of the document and complete the missing mRNA and protein sequences. (You could also do it on paper if you prefer). Translation Worksheet