Bio Study Guide for Midterm 3
Bio Study Guide for Midterm 3 BIOL 1005
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This 8 page Study Guide was uploaded by Leor Clark on Sunday October 9, 2016. The Study Guide belongs to BIOL 1005 at Virginia Polytechnic Institute and State University taught by Dr. Jerry Via in Spring 2016. Since its upload, it has received 365 views. For similar materials see General Biology in Biology at Virginia Polytechnic Institute and State University.
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Date Created: 10/09/16
Bio Study Guide Midterm 3 1. Chapter 9.1 and 9.2 a. The Structure of DNA i. Discovered by Francis Crick and James Watson in the 1950s ii. Nucleotides are the building blocks of DNA 1. Deoxyribose: 5-carbon sugar 2. Phosphate group 3. Nitrogenous base iii. Double-helix: two strands twisted around each other 1. Purine and pyrimidine pair together a. AT b. GC 2. Chargaff’s rule: there is as much A as T and as much G as C because they are complementary b. The Structure of RNA i. Does not contain thymine, does contain adenine, cytosine, and guanine ii. Single-stranded molecule iii. Three types: 1. Messenger RNA (mRNA) 2. Transfer RNA (tRNA) 3. Ribosomal RNA (rRNA) c. How DNA is arranged in the Cell i. Twisted in double helix and supercoiled ii. Prokaryotes: single, circular chromosome that is found in the nucleoid0 iii. Tightly packed chromosomes are darker stained and aren’t active iv. Loosely packed are lightly stained and are active d. DNA Replication i. When a cell divides, each daughter cell receives an identical copy of the DNA ii. Occurs during synthesis phase of cell cycle before entering mitosis or meiosis iii. Complimentary strands = having one strand means being able to recreate the other strand (each strand is a template for the complementary strand to be copied) iv. Semiconservative replication: each new strand of DNA has one daughter strand and one parent strand e. DNA Replication in Eukaryotes i. 3 main stages 1. Initiation a. DNA is made accessible to the proteins and enzymes involved in the replication process b. Origins of replication (specific nucleotide sequences) c. Binds with certain proteins d. Helicase: enzyme that unwinds and opens up the DNA helix e. Replication forks: y-shaped structures that are formed after DNA opens up 2. Elongation: a. DNA polymerase (enzyme) adds DNA to 3’ end of template b. Primer sequence is added with complementary RNA nucleotides i. Primer is removed later and RNA is replaced with DNA ii. Okazaki fragments: new strand put together in short pieceshave repetitive sequien 1. Requires primer made of RNA iii. Lagging strand: strand with the Okazaki fragments 3. Termination: primers are removed a. DNA ligase: enzymes that seal the gaps between fragments ii. Summary of Steps 1. DNA unwinds at the origin of replication 2. New bases are added to the complimentary parental strands; one strand is made continuously while other strand is made in pieces 3. Primers are removed, new DNA nucleotides are put in place of the primers and the backbone is sealed by DNA ligase iii. Telomere Replication 1. Leading strand synthesis continues until end of chromosome is reached 2. Lagging strand no place for primer to be made for DNA fragment to be copied at the end of the chromosome 3. End remain unpaired ends get shorter as they continue to divide 4. Telomeres: ends of the linear chromosomes a. Have repetitive sequences that do not code for particular gene b. Shortened with each round of DNA replication instead of genes 5. Telomerase: enzyme, attaches to end of the chromosome a. RNA template is added to DNA strand, successfully elongated, chromosomes can now replicate b. Active in germ cells, adult stem cells, and some cancer cells c. Discovered by Elizabeth Blackburn in 2009 d. Not active in adult somatic cells e. Associated with aging f. Has potential to treat age-related illnesses f. DNA replication in prokaryotes i. Prokaryotic chromosome = linear, highly coiled around proteins ii. Eukaryotic chromosome = linear, highly coiled around proteins iii. Prokaryotes replicate much more rapidly g. DNA repair i. Most mistakes are corrected ii. Mismatch repair: enzymes recognize wrongly incorporated base and excise it from the DNA, replacing it with the correct base iii. Nucleotide excision repair: DNA double strand is unwound and separated, incorrect bases are removed and replaced 1. people with flaws in this system show sensitivity to sunlight and develop skin cancers early on in life iv. Mutation: when a mistake isn’t corrected 1. Permanent change in DNA sequence 2. Leads to consequences like cancer 2. Lecture 10: DNA Structure and Replication a. What are genes? i. Discovered in late 1800s ii. Discrete units of heritable information iii. Chromosomes: threadlike structure in cells that contain: 1. DNA – 4 nucleotides 2. Protein iv. 50 years ago- are genes made of DNA or protein? b. Fredrick Griffith (1928) i. Researching a vaccine for bacterial pneumonia ii. S Strain (smooth) - virulent iii. R Strain (Rough) – nonvirulent iv. Transformation: Transfer of one or more genes from one organism to another v. Conducted an experiment with the bacteria, killing it rendered it unable to cause disease 1. R-Strain picked up genes from heat- killed S-strain bacteria and were able to kill 2. Did it pick up DNA or proteins? c. Avery McCarty, MacLeod (1944) i. Determined that DNA is the transformation molecule d. Hershey and Chase (1952) i. DNA is the hereditary Molecule ii. Bacteriophage: Virus that infects bacteria 1. Radiolabeled bacteria, sulfur labeled protein and phosphorous labled DNA e. Genes are made of DNA i. Nothing is really known about it yet f. DNA Nucleotides i. 3 parts 1. Phosphate 2. Deoxyribose sugar 3. Nitrogen base ii. 4 different bases 1. Cytosine- single-ring, pyrimidine 2. Thymine- single-ring, pyrimidine 3. Guanine- double-ring, purine 4. Adenine- double ring, purine g. Erwin Chargaff i. A = T ii. C = G h. Pioneering Scientists i. James Watson and Francis Crick ii. Maclyn McCarty iii. Rosalind Franklin i. DNA Double Helix i. Watson and Crick Model ii. Double-stranded (Chains of DNA Nucleotides) 1. Sugar phosphate backbone; covalent bonds iii. Bases have hydrogen bonds iv. Two strands are complementary 1. one sequence of bases can be used to create the correct sequence of bases for the other strand a. strands are antiparallel 2. complementary base pairing 3. 3’ strand and 5’ strand run opposite from one another j. DNA Replication i. All cells come from pre-existing cells ii. DNA must be accurately copied iii. Semiconservative replication: part of parent DNA is conserved in each new DNA molecule iv. Replication fork: formed by opening of the origin of replication v. Helicase: unzips DNA strands vi. RNA primer: synthesized and elongated by DNA polymerase (synthesizes in 5’3’ direction) vii. Leading strand: DNA is synthesized continuously viii. Lagging strand: synthesized in short stretches 1. Okazaki fragments: joins the DNA fragments 2. Synthesis has to go in opposite directions k. Telomeres and Telomerase i. Telomeres: ends of eukaryotic chromosomes; non-coding repetitive sequences 1. The ends of linear chromosomes are maintained by the telomerase enzyme a. Active in most cells of embryos and during childhood development b. Activity is low in adult somatic cells ii. Cancer cells show activation of telomerase iii. Elizabeth Blackburn – discovered telomerase, 2009 Nobel Prize iv. Primase and DNA polymerase synthesize the complementary strand l. DNA Proof reading and repair i. Proofreading by DNA polymerase corrects errors during replication ii. Mismatch repair the incorrectly added base is detected after replication. The mismatch repair proteins detect this base and remove it from new strand. The gap is filled with correct base. 3. Chapter 9.3: Transcription a. Functions of DNA i. Replication ii. Provide info needed to construct necessary proteins necessary for cells to perform functions iii. mRNA: transcribed from DNA, provides code to form a protein by a process called translation b. The Central Dogma: DNA encodes RNA; RNA encodes Protein i. Genes specify sequences of mRNAs ii. mRNAs specify the sequences of proteins iii. Nucleotide is added to mRNA strand for every complementary nucleotide read in the DNA strand iv. Groups of 3 mRNA nucleotides correspond to one amino acid of the protein sequence c. Transcription: from DNA to mRNA i. Eukaryotes genes bound in nucleus transcription occurs in nucleus, mRNA must be transported to cytoplasm ii. Prokaryotes transcription occurs in the cytoplasm iii. Three stages of transcription 1. Initiation a. DNA double helix partially unwinds in the region of mRNA synthesis b. Transcription bubble: region of unwinding c. Promoter: DNA sequence which proteins and enzymes involved in transcription bind to initiate the process i. specific sequence is important because it determines if corresponding gene is transcribed all the time, some of the time, or hardly at all. 2. Elongation a. Template strand: one of the two DNA strands where Transcription always proceeds from b. Non-template strand: mRNA product complementary to the template strand, almost identical to the other DNA strand i. Contains uracil in place of thymine c. RNA polymerase: proceeds along DNA template adding nucleotides by base pairing with the DNA template, except RNA is being synthesized i. DNA is continuously unwound ahead of the core enzyme and rewound behind it. 3. Termination a. Prokaryotic polymerase needs to leave DNA template and free the new mRNA b. Uses two different termination signals c. Process of transcription is now complete iv. Eukaryotic RNA processing 1. Creates a molecule that is much more stable than a prokaryotic mRNA a. Eukaryotic mRNAs last for several hours b. Prokaryotic mRNAs last no more than 5 seconds 2. mRNA transcript is coated in RNA stabilizing proteins a. prevents it from degrading while being processed and exported out of nucleus 3. Elongation is complete enzyme adds string of 200 adenine residues to 3’ end (poly-A tail) a. Protects mRNA b. Signals to cell that transcript needs to be transported to cytoplasm 4. Exons: expressed protein-coding sequences in eukaryotic genes 5. Introns: intervening sequences in eukaryotic genes a. Don’t encode functional proteins b. Removed from pre-mRNA during processing i. Must be completely removed to exons can code the correct amino acids 6. If one single nucleotide is screwed, the protein is nonfunctional 7. Splicing: process of removing introns and reconnection exons a. Occurs while pre-mRNA is still in the nucleus 4. Chapter 9.4: Translation a. Synthesis of protein is a cell’s most energy-consuming metabolic processes b. Translation involves decoding on mRNA message into a polypeptide product c. The Protein Synthesis machinery i. rRNA: ribosomal RNA ii. translation requires the input of an mRNA template, ribosomes, tRNA, and various enzymatic factors iii. ribosomes are complex macromolecules composed of structural and catalytic rRNA, and many distinct polypeptides 1. eukaryotes nucleolus specializes for synthesis and assembly of rRNA iv. ribosomes located in cytoplasm for prokaryotes v. ribosomes located in cytoplasm and ER for eukaryotes 1. made up of small and large subunits vi. tRNA: bound sequentially by large subunits of ribosomes, brings amino acids to growing chain of the polypeptide 1. 40 to 60 types may exist in cytoplasm 2. Translate the language of RNA into the language of proteins d. The Genetic Code i. Triplet codon: three-nucleotide sequence that defines each amino acid ii. Genetic code: the relationship between a nucleotide codon and its corresponding amino acid iii. Combos of nucleotides correspond to single amino acids (encoded by more than one nucleotide triplet) iv. Stop codons: 3/64 codons that terminate protein synthesis and release the polypeptide from the translation machinery v. Start codon initiates translation 1. Ex) AUG – also specifies the amino acids methionine 2. Starts near 5’ end of the mRNA vi. Genetic code is universal 1. Proves that all life on earth shares a common origin e. The Mechanism of Protein Synthesis i. 3 phases ii. Similar in prokaryotes and eukaryotes 1. Initiation a. Formation of initiation complex b. Initiator tRNA interacts with AUG start codon and links to special form of amino acid methionine that is removed from the polypeptide after translation is complete 2. Elongation a. Same for both prokaryotes and eukaryotes b. With each step, a charged tRNA enters the complex, the polypeptide becomes on amino acid longer, and an uncharged tRNA departs 3. Termination a. Occurs when a stop codon (UAA, UAG, UGA) is encountered b. Growing polypeptide is released and the ribosome subunits dissociate and leave the mRNA c. mRNA is degraded so the nucleotides can be reused in another transcription after many ribosomes have completed translation 5. Chapter 9.5: How Genes Are Regulated a. Gene expression: process of turning on a gene to produce RNA and protein b. Cells in multicellular organisms are specialized i. Consequence of different genes in each cell c. Each cell has certain functions they must perform d. Each cell has genes that are not expressed e. Cells will turn on and off genes at certain times in response to changing environments f. Malfunctions in gene expression can lead to diseases like cancer g. Prokaryotic vs. Eukaryotic gene expression i. Prokaryotes 1. lack a cell nucleus 2. Transcription and translation occur almost simultaneously 3. Protein is no longer needed transcription stops 4. Regulation on DNA transcription into RNA is the primary method to control the creation of proteins 5. Gene expression is at transcription level 6. Lac operon: strand of DNA with three adjacent genes that code for proteins that participate in the absorption and metabolism of lactose a. Contains a promoter sequence where RNA polymerase binds to begin transcription b. Operator- area between promoter and three genes ii. Eukaryotes 1. Have intracellular organelles and are much more complicated 2. DNA is in nucleus where it is transcribed in mRNA transported to cytoplasm ribosomes translate it into proteins 3. Transcription and translation are separated by nuclear membrane a. Transcription in nucleus b. Translation in cytoplasm 4. Gene expression can occur in all stages of the process a. Epigenetic level: when gene expression occurs when DNA is uncoiled and loosened from nucleosomes to bind transcription factors b. Transcription level: when RNA is transcribed c. Post transcription level: when RNA is processed and exported to the cytoplasm after it is transcribed d. Translational level: when RNA is translated into protein e. Post translational level: after protein has been made 5. Includes addition of 5’ cap, poly-A tail, and excision of introns and splicing of exons
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