Molecular Genetics DNA Replication PDF

8/27/24, 8:26 PM Platform | Study Fetch Molecular Genetics DNA Replication (00:37 - 00:49) DNA replication occurs during the S phase of the cell cycle, as compared to G1, G2, or M phase DNA replication occurs in 3 stages:...

8/27/24, 8:26 PM Platform | Study Fetch Molecular Genetics DNA Replication (00:37 - 00:49) DNA replication occurs during the S phase of the cell cycle, as compared to G1, G2, or M phase DNA replication occurs in 3 stages: initiation, elongation, and termination Initiation (00:49 - 01:13) Initiation begins at origins of replication, which are specific regions of the DNA At these origins, the DNA strands separate from each other, preparing to form new strands Elongation (01:13 - 02:20) Key players in DNA replication elongation: DNA primase RNA primer DNA ligase DNA polymerase Helicase Topoisomerase Helicase breaks the hydrogen bonds between the antiparallel DNA strands, creating the replication fork Topoisomerase helps relieve the tension and supercoiling in the DNA as it unwinds RNA primase creates RNA primers to provide a starting point for DNA polymerase DNA polymerase 3 synthesizes the new DNA strands in the 5' to 3' direction The leading strand is synthesized continuously, while the lagging strand is synthesized in Okazaki fragments DNA polymerase 1 removes the RNA primers and replaces them with DNA DNA ligase seals any nicks in the DNA backbone Termination (03:25 - 03:40) DNA replication terminates at the telomeres, the long non-coding regions at the ends of DNA molecules Transcription and Translation (00:27 - 00:37) Transcription is the process of copying the genetic information from DNA into RNA Translation is the process of using the RNA to direct the synthesis of proteins https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be8e81bb65113fe36b0/document?go=note 1/7 8/27/24, 8:26 PM Platform | Study Fetch Genetics of Bacteria and Viruses (00:27 - 00:37) Bacteria and viruses have unique genetic structures and mechanisms compared to eukaryotic cells This section will explore the genetics of these simpler organisms Telomeres and Chromosome Shortening (00:03:40 - 00:03:54) When the replication fork reaches the end of the chromosomes, it will terminate there This causes the loss of some telomeres, which are the protective caps at the ends of chromosomes As a result, the chromosomes will shorten a little bit with each round of replication Cells will stop dividing after a certain point unless they have activated telomerase, an enzyme that can repair the telomeres Eukaryotic Transcription (00:03:54 - 00:04:31) Transcription is the process of DNA being turned into RNA Translation is the process of RNA being turned into proteins In eukaryotic transcription: The DNA has a promoter, enhancer, exons, and introns This is transcribed into an unprocessed mRNA that still has the intron sequences Through processing, the 5' cap and 3' poly(A) tail are added, and the introns are spliced out Stages of Eukaryotic Transcription (00:04:31 - 00:04:55) Eukaryotic transcription has three main stages: 1. Initiation: RNA polymerase binds to the promoter sequence, which is enhanced by enhancers 2. Elongation: The transcription bubble forms, and RNA polymerase transcribes the DNA in the 5' to 3' direction 3. Termination: When RNA polymerase reaches a termination signal, the mature mRNA is released Post-Transcriptional Modifications (00:04:55 - 00:06:36) 5' Capping: Adds a 5' cap to the mRNA to prevent degradation and aid in translation Polyadenylation: Adds a poly(A) tail to the 3' end of the mRNA to stabilize it Splicing: Removes the intron sequences from the unprocessed mRNA, leaving only the exons "One of the ways that our cells can tell whether a RNA was introduced by a virus or whether it was made by the cell is the presence of this five prime and three prime cap." https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be8e81bb65113fe36b0/document?go=note 2/7 8/27/24, 8:26 PM Platform | Study Fetch Prokaryotic Transcription (00:06:52 - 00:07:20) Prokaryotic transcription can occur in operons, which are clusters of genes under the control of a single promoter The operator region regulates the promoter by binding to activators or repressors, which can turn the operon on or off Eukaryotic Transcription Prokaryotic Transcription Occurs in the nucleus Occurs in the cytoplasm Has introns and exons Typically does not have introns Requires post-transcriptional modifications Does not require extensive modifications Regulated by enhancers and promoters Regulated by operons and the operator region The Lac Operon (00:07:20 - 00:07:31) The lac operon is a classic operon found in bacteria that controls the metabolism of lactose. (00:07:31 - 00:07:42) The lac operon includes the genes lac Z, lac Y, and lac A, which code for proteins involved in lactose metabolism. These genes are regulated to only be expressed in the presence of lactose. (00:07:42 - 00:07:53) The lac operon responds to specific cellular conditions. (00:07:53 - 00:08:07) Potential conditions that can affect the lac operon include: Low glucose, high lactose High glucose, low lactose Low glucose, low lactose High glucose, high lactose (00:08:07 - 00:08:19) In the absence of lactose, the repressor binds to the operator, preventing RNA polymerase from transcribing the operon. In the presence of lactose, lactose binds to the repressor, causing it to move off the operator and allowing transcription. (00:08:19 - 00:08:30) Glucose is the preferred sugar, so the cell also needs to sense glucose availability. https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be8e81bb65113fe36b0/document?go=note 3/7 8/27/24, 8:26 PM Platform | Study Fetch (00:08:30 - 00:08:46) The cAMP-CAP complex binds to the promoter and enhances RNA polymerase activity when glucose is low. This further increases expression of the lac operon genes. (00:08:46 - 00:09:00) CAP is a protein that binds to cAMP (cyclic AMP), which indicates low energy levels in the cell. The cAMP-CAP complex then binds to the promoter to stimulate RNA polymerase. (00:09:00 - 00:09:14) cAMP is adenosine monophosphate, as opposed to the higher energy ATP. Low ATP and high cAMP levels signal the cell to metabolize lactose for energy. (00:09:14 - 00:09:42) The combination of lactose removing the repressor and cAMP-CAP enhancing RNA polymerase maximizes expression of the lac operon genes. (00:09:42 - 00:10:01) The lac operon is regulated by two mechanisms: 1. Lactose binding to the repressor to allow transcription 2. cAMP-CAP binding to the promoter to enhance transcription The Trp Operon (00:10:01 - 00:10:13) The trp operon is also a repressible operon, similar to the lac operon. (00:10:13 - 00:10:31) The trp operon codes for the enzymes involved in tryptophan synthesis. In the presence of tryptophan, the trp repressor binds to the operator, preventing transcription of the operon. (00:10:31 - 00:10:43) The binding of tryptophan to the trp repressor prevents the creation of more tryptophan. (00:10:43 - 00:11:04) The trp operon also has a mechanism where low or high levels of tryptophan can modulate the mRNA structure and change the way the enzymes are translated. Transcription and Translation Transcription in Bacteria (00:11:04 - 00:11:19) In bacteria, the ribosome can sit on the RNA as it is being transcribed The ribosome moves down the RNA as it is being transcribed https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be8e81bb65113fe36b0/document?go=note 4/7 8/27/24, 8:26 PM Platform | Study Fetch Regulation of Translation by Tryptophan Levels (00:11:19 - 00:11:30) If tryptophan levels are high, the ribosome will move quickly, forming a stem loop This stem loop will cause stalling of translation of the mRNA (00:11:30 - 00:11:49) If tryptophan levels are low, the ribosome will stall when it needs to add a tryptophan This will cause an alternative stem loop to form, leading to full translation of the mRNA This is a way to attenuate the signal in the tryptophan operon Structure of Ribosomes (00:12:01 - 00:12:20) Prokaryotic ribosomes have a 50S and 30S subunit, totaling 70S Eukaryotic ribosomes have a 60S and 40S subunit, totaling 80S (00:12:20 - 00:12:33) Mnemonic for ribosome subunits: Eukaryotic: 60S + 40S = 80S Prokaryotic: 50S + 30S = 70S (00:12:33 - 00:12:45) The S in the subunit names stands for Svedberg units, a measure of sedimentation rate Codons and the Genetic Code (00:12:45 - 00:13:12) Codons are triplets of nucleotides that code for individual amino acids It's important to memorize the start codon (AUG) and stop codons (UAA, UAG, UGA) (00:13:12 - 00:13:24) Mnemonic for stop codons: "You go away, you are annoying, and you are gone." The Process of Translation (00:13:24 - 00:13:48) tRNA carries the appropriate amino acid to the ribosome tRNA synthetases attach the amino acid to the correct tRNA (00:13:48 - 00:14:06) There is a tRNA synthetase for each amino acid to attach it to the proper tRNA (00:14:06 - 00:14:19) The ribosome has three sites: the A site (entry), P site (peptide formation), and E site (exit) (00:14:19 - 00:14:37) https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be8e81bb65113fe36b0/document?go=note 5/7 8/27/24, 8:26 PM Platform | Study Fetch The codon in the mRNA pairs with the complementary anticodon on the tRNA, bringing the amino acid to the ribosome (00:14:37 - 00:14:51) Overview of the translation process: Codon in mRNA Anticodon on tRNA Amino acid carried by tRNA Ribosome catalyzes peptide bond formation Protein Synthesis: Transcription and Translation Transcription and Translation Overview (00:14:51 - 00:15:03) The mRNA sequence is read by the ribosome The ribosome recognizes the start site (AUG) on the mRNA The ribosome then proceeds to add amino acids one by one, forming the polypeptide chain Elongation of the Polypeptide Chain (00:15:03 - 00:15:14) tRNA carrying amino acids enters the A site of the ribosome The peptide bond forms at the P site The tRNA exits the E site after donating its amino acid The uncharged tRNAs return to the aminoacyl-tRNA synthetases to be recharged with amino acids Schematic of Elongation (00:15:14 - 00:15:30) The mRNA moves through the ribosome, with each codon being translated into an amino acid The polypeptide chain is elongated as this process continues Schematic of Elongation (Continued) (00:15:30 - 00:15:41) The ribosome has three sites: A (amino acid), P (peptide), and E (exit) The tRNA carrying the growing polypeptide chain moves through these sites during elongation Mutations in Codons https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be8e81bb65113fe36b0/document?go=note 6/7 8/27/24, 8:26 PM Platform | Study Fetch (00:15:52 - 00:16:29) Mutations can occur due to errors in DNA or external factors like radiation Types of mutations: Silent mutation: No change to the amino acid Nonsense mutation: Introduces a stop codon Missense mutation: Changes the amino acid Genetics of Bacteria and Viruses (00:16:29 - 00:16:57) Bacterial viruses (bacteriophages) have a head, tail, and tail fibers Eukaryotic viruses like adenovirus and HIV also have a defined structure Viral Reproduction Cycles (00:16:57 - 00:17:13) Lytic cycle: Virus destroys the host cell Lysogenic cycle: Virus uses the host cell to replicate but remains dormant Bacterial Conjugation (00:17:13 - 00:17:38) Bacteria can transfer plasmids to other bacteria through a process called conjugation This involves the use of a pilus to connect the cells and transfer the plasmid Horizontal Gene Transfer (00:17:38 - 00:18:18) Bacteria can acquire new genetic material through various mechanisms: Transduction: Infection by a virus Transformation: Uptake of free DNA from the environment Conjugation: Transfer of plasmids between bacteria Mastering Molecular Genetics (00:18:18 - 00:18:30) Congratulations! You have now mastered the key concepts of molecular genetics. https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be8e81bb65113fe36b0/document?go=note 7/7