Replication of DNA, Transcription, and Translation and the Code
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| 557847747 | Replication of DNA | Copying of DNA into DNA. There's a parent DNA molecule of two strands. The first step in replication is the separation of the two strands: "melting the DNA". Then, each strand serves as a template to form a new complementary strand. (Templated polymerization via complimentary pairing.) Lastly, the nucleotides connect to form united sugar-phosphate backbone. Each "daughter" DNA molecule is one parental strand+one new strand. | |
| 557847748 | Patterns of Replication | There were different models of DNA replication. The semiconservative model is the one that turned out to be correct. (Two with one parent strand and one daughter strand). Conservative model: (One with both parent strands and one with both daughter strands). Dispesive model: Bits and pieces mixed for the daughter strands. | |
| 557847749 | Meselson-Stahl Experiment | Concluding whether replication is conservative or semi-conservative. Cultured bacteria in N15 medium. Then put it in N14 medium so the N15 DNA and N14 DNA would mix. Put it in Cesium Chloride with concentration gradient and after two generations, half was at top, N14, and half was in the middle N14/N15 | |
| 557847750 | Sedimentation of DNA (CsCl gradients) | Isolate DNA and put in cesium chloride. Put in centrifuge and put on high speed. A concentration gradient will form and N-15 heavy DNA will be at the bottom and lighter N-14 towards the top. | |
| 557847751 | DNA polymerase | An enzyme that copies DNA. Prokaryotes have 5 different sorts: Pol I-PolV and eukaryotic cells have four sorts: α,β,γ, & δ. | |
| 557847752 | (Pol III) Prokaryotic | Reads the template strand and adds a complimentary nucleotide. Reads 3' to 5', but synthesizes in 5' to 3' direction. Proofreads in case a nucleotide is incorrectly added. | |
| 558951736 | Bilateral Synthesis | In eukaryotes, DNA starts to replicate in several spots called origins of replication. At these origins in the bubble, the daughter strand forms in either direction. It ends in two daughter molecules. | |
| 558960901 | Replication Fork | The point where the helicase is being untwisted simultaneously with the production of the daughter cell. There's one on either side of the bubble. In eukaryotic cells, replication occurs at many different sites along the DNA molecule. | |
| 558960902 | Leading Strand | Recall that with DNA, one strand is 5----3 and the other one is 3---5. DNA polymerase reads the 3---5 strand and copies it 5---3. This strand is the leading strand. | |
| 558995049 | Lagging Strand | The lagging strand is also created in a 5---3 direction. As the helicase unwinds, the lagging strand is synthesized discontinuously. Primase creates an RNA primer that is extended by DNA polymerase. These extended primers are called okazaki fragments and they are made continuous by DNA ligase. | |
| 558995050 | Okazaki fragment | A short segment of DNA synthesized on a template strand during DNA replication. Many Okazaki fragments make up the lagging strand of newly synthesized DNA. | |
| 558995051 | Enzymes involved in Model of Replication in Bacteria with DNA Pol III | Helicase, topoisomerase, single strand binding proteins, primase, POL III, DNA Pol I, DNA ligase | |
| 558995052 | Helicase | Enzyme that untwists the DNA helicase | |
| 558995053 | Topoisomerase | A protein that functions in DNA replication, helping to relieve strain in the double helix ahead of the replication fork. (removes supercoils) | |
| 558995054 | Single Stranded Binding Proteins | Stabilize the replication fork, keep it from coiling back up again | |
| 558995055 | Primase | Forms RNA primer pieces | |
| 558995056 | Pol III | Synthesizes new DNA strands. It copies both strands simultaneously. It's a replisome that does the lagging/leading aka continuous/discontinuous strands simutaneously. | |
| 558995057 | DNA Polymerase I | Removes the RNA piece and fills in the gap with complimentary nucleic bases | |
| 558995058 | DNA ligase | seals the lagging strand, joins the okazaki fragments | |
| 558995059 | The Structure of DNA Polyermase III | A dimer consisting of 10 proteins. The dimer consists of an inner proofreading subunit (E) and catalytic subunit (a). Each half of the dimer encircles forms a clamp that encircle the DNA template and move the DNA through the catalytic unit like a rope through a ring. | |
| 558995060 | DNA repair | A nuclease enzyme cuts out the portion of the damaged DNA. Then DNA poly. III repairs the strand by filling in new proper nucleotides. Then DNA ligase seals the free end of the new DNA to the old portion to complete the strand. | |
| 559016499 | Central Dogma of Molecular Biology | Depicts the flow of genetic information. Transcription is the copying of DNA sequences into RNA. Then translation is the copying of RNA sequences into proteins. | |
| 559016500 | DNA----->Protein | DNA Sequence (TAC)--->RNA Sequence (AUG)---->Amino Acid Sequence (MET). This means a triplet sequence in DNA becomes a codon in mRNA which becomes an amino acid in protein. Notice that in RNA, U is used instead of T. | |
| 559016501 | Central Dogma of Molecular Biology in Prokaryotes | Within the prokaryotic cell, DNA is transcribed into mRNA, which translates into the appropriate amino acid/protein by using the housing site of the ribosome. | |
| 559016502 | Central Dogma of Molecular Biology in Eukaryotes | Much like how it occurs in prokaryotes, except that the transcription process is isolated into the nucleus. Then, the transcribed mRNA leaves the nucleus to the ribosome where it's translated into proteins. | |
| 559016503 | DNA vs RNA | DNA uses a deoxyribose sugar and RNA uses a ribose sugar. For bases, DNA uses thymine (T) while RNA uses uracil (U). DNA is double stranded and RNA is single stranded. | |
| 559016504 | One gene-one enzyme hypothesis | Each gene codes for one enzyme that affects just a single step in the body's various metabolic pathways | |
| 559016505 | Transcription | Occurs via RNA polymerase. | |
| 559016506 | RNA polymerase | Catalyzes the synthesis of RNA on a DNA template. The enzyme has three polypeptide subunits: alpha, beta, and beta' in a stoichiometry of A2BB' and an additional subunit, omega. This RNA polyermase binds onto DNA and catalyzes the synthesis of RNA. Has no specificity without fifth subunit, the sigma factor. | |
| 559016507 | Subunits of RNA Polyermase (Alpha) | Required for the assembly of the enzyme. It interacts with some regulatory proteins and is involved in catalysis. | |
| 559016508 | Subunits of RNA Polyermase (Beta) | Involved in catalysis, chain initiation, and elongation | |
| 559016509 | Subunits of RNA Polyermase (Beta Prime) | Binds to the DNA template. | |
| 559016510 | Subunits of RNA Polyermase (Sigma) | Initiates specificity for RNA AND directs the enzyme to a promoter so that is can code nucleotides | |
| 559016511 | Subunits of RNA Polyermase (Omega) | Required to restore denatured RNA polymerase in vitro to its fully functional form | |
| 559035758 | Stages of Transcription | Enzyme binds to the promoter at the starting point. Then....Initiation: DNA is unwound and RNA begins to be transcribed. Elongation: DNA continues to unwind with the path of RNA enzyme and the RNA transcript lengthens. Lastly, termination happens. The RNA enzyme falls off and the helicase rewinds. Then, you have a resulted complete RNA molecule | |
| 559057404 | The Sense Strand and The Antisense Strand | Has an RNA version of its sequence translated or translatable into proteins. When RNA polymerase acts upon the DNA strand, the completed mRNA has the same nucleotide sequence as the sense strand. | |
| 559057405 | Antisense Strand | The template strand. It is transcribed and creates the mRNA to be translated into a protein. It is the complement to the sense strand. | |
| 559278681 | Ribosome Structure | The ribosome consists of a large subunit on top and a small subunit on the bottom. There are three sites within the ribosome. E, P, and A. E=Exit Site where the mRNA exits. P=Peptidyl-tRNA binding site. A site=Aminocyl-tRNA binding site. | |
| 559278682 | Messenger RNA (mRNA) | Carries information specifying amino acid sequences of proteins from DNA to ribosomes. It codes for amino acid sequences | |
| 559278683 | Transfer RNA (tRNA) | Functions as an adapter molecule for protein synthesis. Translates mRNA codons into amino acids. It is small and single stranded with a secondary structure. It picks up AA and transports it to ribosomes. (Anticodon sequence) | |
| 559278684 | Ribosomal RNA (rRNA) | Plays catalytic (ribozyme) roles and structural roles in ribosomes. 3 different pieces of rRNA come together to create the ribosome | |
| 559278685 | Primary Transcripts | A precursor to mRNA, tRNA, of rRNA before being spliced or cleaved. (Some intron RNA can act as a ribozyme, catalyzing its own splicing.) Large 1:1 RNA copy of DNA genes that function as the precursor to mRNA molecules....the RNA before it's spliced. | |
| 559278686 | Split Gene/Interrupted Gene | Approximately 94% of human genes are thought to be split. mRNA strand is shorter than its template DNA so it's not encoded colinearly. Instead, the DNA molecule has loops of uncoded/unexpressed DNA called introns. | |
| 559278687 | Introns | Nucleotide sequence in a gene that is NOT EXPRESSED. It is stored in loops and does not make it to the mRNA to go to the ribosomes and code for amino acids. Purpose of introns still being investigated, but estimates suggest 98.8% of DNA does not code. | |
| 559278688 | Exons | Nucleotide sequence in a gene that remains present when mRNA is transcribed. It is the EXPRESSED part of the gene that codes for amino acids | |
| 559278689 | Processing/Cutting of Introns and Extrons | When mRNA is transcribed it's a primary transcript, RNA with the introns still there. The introns are cut out and the exons are spliced together. This is called RNA processing. | |
| 559278690 | Spliceosome | A complex of snRNA and protein subunits that removes introns from a transcribed pre-mRNA segment. That process is called splicing. | |
| 559278691 | mRNA Structure | the pre-mRNA begins with a 5' cap and ends with a poly-A tail. Within, there are coded regions (exons) and uncoded regions (introns). There are start codons (AUG) and stop codons (UGA) on either side of the exons. | |
| 559764266 | Role of the 5' Cap and the Poly-A tail | An experiment done showed that the purpose to the cap and tail is to preserve the stability and strength of the data within. Defensive measures. | |
| 559764267 | Nuclear Export of Mature mRNA | mRNA leaves nucleus through a nuclear core complex. A Cap binding protein latches onto the cap and a poly-A binding proteins binds onto the poly-A tail. EJC proteins bind within on the DNA. Collectively, they bind, signal that the RNA is ready for export, and facilitate its exit. When it exits, there's a protein exchange on the 5' cap called the initiation factor for protein synthesis. (Translation) | |
| 559764268 | Differences Between Prokaryotes and Eukaryotes (RNA processing and transcription) | In Eukaryotic cells, transcription occurs in the nucleus and has to exit through the nuclear pore complex. Also, in prokaryotes, the whole splicing, capping, mRNA processing doesn't occur. | |
| 559764269 | snRNP | Small nuclear RNA plays a structural and catalytic role in spliceosome. They are adorably called snurps and there are 5 making up a spliceosome. [U1, U2, U4, U5 & U6] | |
| 559764270 | Signal Recognition Particle (SRP) | Some proteins need to go to the ER for modification with sugars. They do this simultaneously with their synthesis. The peptide being synthesized will have a signal peptide that is recognized by the SRP. The SRP guides it to the ER membrane. | |
| 559764271 | Small nucleolar RNA (snoRNA) | Aids in processing pre-RNA transcripts for ribosome subunit formation in the nucleolus | |
| 559764272 | Mircro RNAs (miRNA) | Very small molecules of RNA that are noncoding. They work to interfere with protein expression. Structurally, they form stem-loop structures and there's more than 400 known ones in the human genome. (siRNA and miRISC are examples of miRNAs.) | |
| 559764273 | siRNA / miRISC | RNA induced silencing complex/ Silencing RNA....they approach the target RNA and keep it from expressing itself either by degrading the DNA or by blocking its translation. | |
| 559764274 | Euchromatin | the ACTIVE form of chromosomal DNA | |
| 559764275 | Heterochromatin | the INACTIVE form of chromosomal DNA | |
| 559764276 | Barr Body | With females: XX (two doses of genetic activity). With males: XY (one dose of genetic activity), but females don't have double the genetic expression. Why? Because one of the X chromosomes transcriptionally inactive. Which X becomes inactive appears random. This inactive X is called the BARR BODY. | |
| 559764277 | How does the X chromosome become inactive? | It grows inactive due to Chromatin Condensation because of three mechanims. (Methylation, chromatin proteins that promote heterochromatization, and the action of a single gene on one X. When that one gene is active, it makes a microRNA....miRISC | |
| 559764278 | Xist gene | only slightly methylated, makes siRNA for further interference. is NOT mRNA. | |
| 559764279 | Xist-siRNA | Binds to the X-chromosome it was transcribed from and encourages inactivation of the X-chromosome. Once inactive, all its progeny (genetic descendants) are inactive as well. | |
| 559764280 | How do active X-chromosomes prevent the action of siRNA? | There's an anti-Xist gene called Tsix that makes an RNAi that binds complimentarily to the siRNA-Xist molecule. This makes it double stranded and inactivates it. | |
| 559764281 | Gene Imprinting | The inactivation of alleles, switching off alleles. They can increase risk of disease if a child receives a silenced allele of a gene. If the active allele is destroyed, there's no backup because the other one is silent. | |
| 559764282 | Probing Gene Function | Scientists have found that they can probe and manipulate gene function by transfecting synthetic siRNAs to suppress various genes from being translated. | |
| 559764283 | Translation (Making a Protein) | the process of making a a protein with a specific amino acid sequence from a unique mRNA sequence. | |
| 559764284 | Where are polypeptides built? | On the ribosome on a polysome. (A polysome is a cluster of ribosomes working on an mRNA molecule.) | |
| 559764285 | Sequence of 4 Steps in Translation | 1. Add an AA to tRNA. (Activation) 2. Assemble Players. (Initiation) 3. Add new AAs (Elongation) 4. Stop the process. (Termination) | |
| 559764286 | Structure of tRNA | Coiled RNA with an amino acid attatched at the 3' end. It coils in so that stems are created by hydrogen bonds between base pairing. The loops consist of unpaired bases | |
| 559764287 | Activation | Occurs when an amino acid is joined to tRNA when they both enter the Aminoacyl-tRNA synthetase. ATP is used for this. When it exits, it's Aminoacyl tRNA, or aa-tRNA.... "charged tRNA". | |
| 559764288 | Initiation | With the mRNA bound to the small ribosomal unit, the initiator tRNA latches on to the start codon on the P site. The resulting tRNA on the P-site is called the translation initiation complex. GTP is needed for this to occur. GTP---->GDP | |
| 559764289 | Elongation | Amino acids are added via peptidyl transferase (a ribozyme). There's tRNA in the P site. The anticodon recognizes the next codon in the mRNA and binds there. With GTP---->GDP, the polypeptide on the P-site moves to join the one amino acid on the A site. Now that the new amino acid is attached, the empty tRNA in the P site goes to the E-site and leaves. Then, the tRNA in the A site goes to the P-site to await next aminoacyl tRNA | |
| 559764290 | Termination | When the final amino acid is added to the polypeptide and jumps to the P-site, the stop codon attracts a protein called the release factor. Stop codons: UAG, UAA, UGA) There's no corresponding aa-tRNA. The tRNA is released and the polypeptide is released. Then, with 2 GTP, the large subunit, release factor, mRNA, and small subunit break apart, waiting for next piece of mRNA to be read. | |
| 559764291 | Genetic Code | The sequence of nucleotides in DNA. Generally shown as mRNA coding format. It specifies the order that amino acids are to be synthesized to the polypeptide. | |
| 559764292 | Coding Ratio | Scientists knew there were 20 amino acids that existed, 20 that needed to be coded. So then they had to figure out how many nucleic cases translated into an amino acid. It had to be 3. If it was one, there would only by 4 possibilities. If it was two, there's only 16 amino possibilities. If it's three, then 4x4x4=64. More than enough options for coding | |
| 559764293 | The 64 possible codons | 61 of the 64 codons actually code for an amino acid. One of them, AUG is an initiator, or stop codon. Three of them, UGA, UAA, and UAG are stop codons. This code is universal and redundant. (Multiple codons code for the same amino acid.) |
