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by: Shira Clements


Shira Clements

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About this Document

Transcription, Translation, Central dogma
Principles of Biology I
Norma Allewell
Class Notes
Science, Biology
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This 8 page Class Notes was uploaded by Shira Clements on Friday March 25, 2016. The Class Notes belongs to BSCI105 at University of Maryland taught by Norma Allewell in Fall 2015. Since its upload, it has received 39 views. For similar materials see Principles of Biology I in Biology at University of Maryland.


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Date Created: 03/25/16
Shira Clements BSCI105 Chapter 17 From Gene to Protein Overview of Flow of Genetic Information - DNA inherited by organism leads to specific traits by dictating synthesis of proteins and of RNA molecules involved in protein synthesis - Gene expression- process by which DNA directs synthesis of proteins o two stages- transcription and translation Garrod- first to suggest that genes dictate phenotype through enzymes that catalyze specific reactions, disease can be caused by not being able to create a certain enzyme - genes dictate production of enzyme Many eukaryotic genes can code for a set of closely related polypeptides via alternative splicing. Few genes code for RNA molecules that are imp to cell but not translated into protein. Basic Principles of Transcription and Translation - Gene does not build protein directly, just give instructions - Nucleic acid RNA (ribose and U base and single strand) is bridge between DNA (deoxyribose and T base and double strand) and protein - Both nucleic acids and proteins are polymers that convey information o DNA/RNA- monomers are 4 types of nucleotides that differ in bases and genes are many nucleotides long o Proteins- monomers are amino acids o Both have different languages but convey information, so need transcription and translation to convert from DNA to protein Occurs in both Transcription- synthesis of RNA using information from DNA, eukaryotes and prokaryotes, just in rewritten in RNA form prokaryotes they - DNA template serves as template for making the happen at same complementary RNA strand, time because not o For protein coding gene- it is mRNA that is synthesized organelles but in eukaryotes it is at since it carries genetic information from DNA to protein different times- synthesizing machinery transcription in o Eukaryotes- it makes pre-RNA or primary transcript nucleus and and then other processes occur to make it mRNA translation in Translation- synthesis of polypeptide using information from mRNA cytoplasm - Change in language- nucleotide sequence to amino acid - Occurs in ribosomes Central Dogma- DNA to RNA to protein Genetic Code - only four nucleotide bases but 20 amino acids, so how can it be that DNA makes specific protein? - multiple nucleotides correspond to one amino acid. - Triplets of nucleotide bases are the smallest number of units that can 3 code for amino acid, allows there to be 64 (4 ), which is more than enough combinations= triplet code- series of words in a gene is transcribed into complementary series of three nucleotide words in mRNA, then translated into amino acid. o mRNA nucleotide triplets= codon and written in 5’ to 3’ o more than one codon can indicate one amino acid o need to make sure it is read correctly because if one base is missing, everything is thrown off - In transcription- only one strand of DNA is being transcribed= template strand, which provides pattern for sequence on nucleotides in an RNA transcript - mRNA is complementary, not identical, to template- base pairing, synthesized antiparallel o U is in RNA instead of T in DNA as a base and ribose is in RNA instead of deoxyribose in DNA as a sugar o 3’-ACC-5’ synthesizes 5’-UGG-3’ - During translation- codons are decoded/translated into sequence of amino acids o Codons are read in 5’ to 3’ along mRNA o If there are 300 nucleotides, there will be 100 amino acids in polypeptide chain o 3 codons- do not designate amino acids- stop signals to end translation- UAA, UAG, UGA o start codon- initiations signal- mRNA codon AUG, to begin translating Transcription DNA directs synthesis of RNA mRNA (carrier of information from DNA to cell protein synthesizing machine) is transcribed from template gene - RNA polymerase- enzyme separates two strands of DNA and joins RNA nucleotides complementary to DNA template strand o Can only assemble in 5’ to 3’ direction o Able to start from scratch, no primer necessary - Promoter- DNA sequence where RNA polymerase attaches and starts transcription - Terminator- signal that ends transcription (downstream from promoter) - Transcription unit- the stretch of DNA that is transcribed into an RNA sequence - Prokaryotes have one type of RNA polymerase and eukaryotes have three types o mRNA synthesis is RNA polymerase II - Initiation- promoter of gene includes- start point- nucleotide where RNA synthesis actually happens- and extends several dozen or more nucleotide pairs upstream from start point. RNA polymerase binds to promoter and determines where transcription starts and which strand is used as template o Bacteria- RNA polymerase binds to promoter itself o Eukaryotes- collection of proteins (transcription factors) mediate binding of RNA polymerase and initiation of transcription- once transcription factors are attached to promoter, then RNA polymerase II binds to it. Whole complex= transcription initiation complex.  TATA Box- crucial promoter DNA sequence  Protein-protein interactions are crucial in controlling eukaryotic transcription- ex- interaction between eukaryotic RNA polymerase II and transcription factors - Elongation- RNA polymerase moves along DNA and untwists the double helix, it adds nucleotides to 3’ end of growing RNA molecule, synthesizing RNA and peels away from DNA template and DNA double helix reforms. o More than one polymerase can transcribe a gene, which increase amount of mRNA made, which helps make more protein - Termination- bacteria- transcription goes through terminator sequence in DNA, and the transcribed terminator (the RNA sequence of termination) is the signal and causes polymerase to detach from DNA and release the transcript o Eukaryotes- RNA polymerase II transcribes sequence of DNA called polyadenylation signal (AAUAAA) in pre-mRNA and then at a point 10-35 nucleotides downstream from it, proteins associated with growing RNA transcript cut it free from polymerase, releasing the pre-mRNA which undergoes RNA processing Eukaryotic Cells Modify RNA after Transcription - With pre-mRNA om nucleus, before cytoplasm and it is called RNA processing - Alterations of mRNA ends- 5’ end gets a 5’ cap, modified form of a guanine (G) nucleotide added on the 5’ end after transcription of first 20-40 nucleotides. o 3’ end- enzyme adds 50-250 A nucleotides forming poly-A tail o both of them- facilitate export of ready mRNA, protect, help ribosomes attach to 5’ end of mRNA once it reaches cytoplasm o UTRs- ends of the 5’ and 3’ ends, but not translated into proteins, but helps with ribosome binding - Split Genes and RNA Splicing-RNA splicing- removal of large portions of RNA that is initially synthesized, which are not continuous with each other. Cut out introns but keep exons, part that is expressed in protein, except for UTR- exons exit nucleus o snRNPS (in nucleus and contain RNA and protein molecules) recognize splice sites (has RNA in there called snRNA and help catalyze)  can join with other proteins to create a spliceosome- almost the size of ribosome, interacts with cites along the intron and releases the intron, and joins the two exons together, creating mRNA o Ribozymes- RNA molecules that function as enzymes, some can splice introns out by themselves  3 reasons why RNA molecules can function as enzymes  RNA is single stranded (and can base pair with others) gives it a particular shape  Has similar functional groups to enzyme  Can hydrogen bond with other nucleic acid molecules adds specificity to its catalytic activity - Alternative RNA splicing- many genes create two of more polypeptide, depending on which sections are treated as exons during RNA processing o Number of proteins produced can be much more than number of genes because of this - Domain- distinct structure and parts of proteins- exons can code for it o One domain might include active site, while another might allow enzyme to bind to cellular membrane - Exon shuffling- exons crossing over to create different protein- mixing with one another Translation - RNA directed synthesis of polypeptide (protein) - Message is the series of codons along an mRNA, and the translator is tRNA (80 nucleotides long)- transfer amino acids from cytoplasmic pool of amino acids to growing polypeptide in ribosome o Ribosomes (made of RNA and protein) adds amino acids brought to it by tRNA to growing end of polypeptide chain o Molecules of tRNA are not all identical and each part of tRNA translates a particular mRNA codon into an amino acid o tRNA arrives are ribosome with amino acid on one side and anticodon (base pairs with a complementary codon on mRNA) on other o codon by codon message is translated as tRNAs deposit amino acids in order prescribed and ribosome joins amino acid into chain o tRNA is translator- read nucleic acid word and interpret it as protein word o tRNA is transcribed from DNA template- eukaryotes- made in nucleus and then goes to cytoplasm where translation occurs- picking up amino acids in cytosol and then adding it to polypeptide chain at ribosome and then leaving ribosomes ready to pick up another amino acid o stretches of nucleotide bases that can hydrogen bond to each other and can fold back onto itself because it is single strand and for a 3D structure (cloverleaf) and then from there twists and fold into L-shaped- at the bottom has an anticodon (base pairs to mRNA codon) and then the other side (5’ end) is the attachment site for amino acid.  Anticodons are written in 3’ to 5’ to align with the 5’ to 3’ codons  3’AAG5’ anticodon pairs with mRNA codon 5’UUC3’ o two instances of molecular translation- 1. tRNA that binds to mRNA codon specifies the amino acid that it has to bring to ribosome  aminoacyl-tRNA synthecase- atches up the correct tRNA and amino acid  active site fits only a specific amino acid sequence and tRNA  20 different ones- ones for each amino acid- can bind to tRNAs that codes for amino acid  catalyzes covalent bond of tRNA and amino acid by hydrolysis of ATP, so now it is a charged tRNA, which is then released from enzyme and available to deliver amino acid to polypeptide chain of ribosome  pairing of tRNA anticodon with appropriate mRNA codon  some tRNAs can bind to more than one specific codon- U can pair with A or G because of the phenomenon wobble- flexible base pairing at specific codon position (U at 5’ end of anticodon can pair with either A or G at 3’ of codon)- explains synonymous codons given for amino acids most often differ in third nucleotide base (anticodon 3’UCU5’ can base pair with mRNA codon 5’ AGA 3’ or 5’AGG3’) - Ribosomes- facilitate specific coupling of tRNA anticodons with mRNA codons during protein synthesis. Both subunits are made up of proteins and rRNA o Eukaryotes- subunits are made in nucleolus o Ribosomal RNA genes are transcribed and RNA is processed and assembled with proteins from cytoplasm and the resulting ribosomal subunits are then exported via nuclear pores to cytoplasm  Subunits only function when they attach to mRNA molecule (bacteria and eukaryotes)- rRNA is most abundant RNA  Eukaryotes’ ribosomes are slightly larger than prokaryotes- differences are significant though small- antibiotic can inactive bacterial ribosome but not inhibiting eukaryotic ribosomes to make proteins. o Structure reflects function of bringing mRNA together with tRNAs carrying amino acids  Has binding site for mRNA and thre binding sites for tRNA  P site- hold tRNA carrying growing polypeptide chain  A site- holds tRNA carrying next amino acid to be added to chain  E site- tRNAs leave ribosomes through this  Holds tRNA and mRNA close to each other and positions new amino acid for addition of carboxyl end of growing polypeptide, and then catalyzes formation of peptide bond. Polypeptides goes through exit tunnel in large subunit - Ribosome Association and Initiation of Translation- brings mRNA (tRNA bearing first amino acid of polypeptide) and two subunits of ribosome together o Ribosomal subunit binds to mRNA and specific initiator tRNA  Bacteria- can happen in either order- binds to mRNA upstream of AUG  Eukaryotes- small subunit with initiator tRNA already bound binds to 5’ cap of mRNA and moves/scans downstream along mRNA until it reaches start codon and then the initiator hydrogen bonds to AUG start codon, which signals translation, & establishes codon reading frame for mRNA o After mRNA, initiator tRNA, and small subunit unite, attachment of large ribosomal subunit occurs= completion of translation initiation complex  Proteins help bring everything together  Cells spends energy obtained by hydrolysis of GTP to form the complex  tRNA now sits in P site and A site is ready for next tRNA  polypeptide is always synthesized from methionine amino acid end (N terminus) to final amino acid end (carboxyl terminus) - Elongation of Polypeptide Chain o Amino acids are added one by one to previous amino acid at C terminus o Needs proteins called elongation factors to add o 3 steps  1. Codon recognition- anticodon of tRNA base pairs with mRNA codon in A site. Hydrolysis of GTP increases accuracy and efficiency of this step.  2. Peptide bond formation- rRNA molecule of large subunit catalyzes formation of peptide bond between amino group of amino acid in A site and C end of growing polypeptide in P site. This removes polypeptide from tRNA in P site and attaches it to amino acid on the tRNA in A site.  3. Translocation- ribosome translocates the tRNA in A site to P site and at the same time, the empty tRNA in P site is moved to E site to be released. mRNA moves along with its bound tRNAs, bringing next codon to be translated into A site o GTP hydrolysis is used in step 1 (codon recognition) and 3 (translocation). o Moves 5’ to 3’- just like mRNA - Termination of Translation- elongation happens until stop codon of mRNA reaches A site o UAG,UAA, and UGA are stop codons, don’t translate into protein o Release factor- protein shaped like tRNA- binds directly to stop codon in A site and calls for addition of water instead of amino acid to polypeptide chain, which breaks bond (hydrolyzes) of completed peptide and tRNA in P site, releasing polypeptide through exit tunnel in large subunit o Remainder of translation then comes apart in multistep process, aided by protein factors and requires hydrolysis of two more GTP molecules. - Single mRNA is used to make many polypeptides at the same time- once ribosome is far enough passed start codon, another can attach to mRNA and translate= polyribosome - Completing and Targeting the Functional Protein- modifications & finishing polypeptides o Protein Folding and Post Translational Modification-  Synthesis- polypeptide chain begins to coil and fold spontaneously because of amino acid sequence (primary sequence), forming protein with specific 3D shape (secondary and tertiary), chaperone helps it fold correctly o Post-translational modifications- other substances can be added to amino acids  Enzymes can remove amino acids from leading end of chain  Enzymes can cleave o Free ribosomes are in cytosol and synthesize proteins that usually stay there o Bound ribosomes are attached to inner side of ER, make proteins of endomembrane system and proteins secreted from cell o Polypeptide synthesis always begins in cytosol and starts to translate mRNA and there the process is completed unless the growing polypeptide itself cues ribosome to attach to ER.  Ones for secretion are marked by signal peptide- targets protein to ER where it can finish translation  Recognized as it emerges from signal recognition particle (SRP) which is a ribosome by a protein RNA complex with a membrane pore and signal cleaving enzyme- once SRP leaves, protein synthesis continues and is still attached to translocation complex  The signal cleaving enzyme cuts off the signal peptide and the rest of the completed polypeptide leaves ribosome and folds into final form  Escorts ribosome to receptor protein in ER 


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