Exam 3 Study Guide
Exam 3 Study Guide 30156
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This 18 page Study Guide was uploaded by Hannah Kennedy on Sunday August 7, 2016. The Study Guide belongs to 30156 at Kent State University taught by Dr. Helen Piontkivska in Spring 2016. Since its upload, it has received 20 views. For similar materials see ELEMENTS OF GENETICS in Biological Sciences at Kent State University.
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Date Created: 08/07/16
Exam 3 Study Guide: © Hannah Kennedy, Kent State University Ch. 11—molecular structure of DNA and RNA 1. Properties of genetic material a. 4 conditions to be met to act as genetic material i. (1): ability to store information necessary to construct the organism ii. (2): replication with high fidelity due to the copy of material as it is passed from parents to offspring and from mother cells to daughter cells iii. (3): need a way to access/express the information iv. (4): needs to be able to experience mutations for evolutional purposes 2. How we know that DNA is the molecule of inheritance a. Experiment #1: Griffith—proved that genetic material is capable of transforming other elements i. injected pathogenic S (smooth) strain into a mouse → dies 1. the S strain is encapsulated and takes over the mouse’s immune system and proliferates into the bloodstream ii. injected non-pathogenic R (rough) strain into mouse → lives 1. the R strain is non-encapsulated and the mouse’s immune system destroys it iii. heat killed S strain injected into mous→ lives 1. this verified that the proliferation of the S strain was causing the mouse to die iv. combined the R strain and a heat-killed S strain and injected into mouse → dies, only S strain is found in tissue 1. this shows the S strain was the transforming principle 2. this occurred bc the live type R bacteria couldn’t alone overtake the mouse’s immune system so the type S transformed the type R a. transformed bacteria acquired the information to make a capsule b. variation exists in ability to create the capsule and cause death c. genetic material necessary to create a capsule must be replicated and transmitted b. Experiment #2: Avery et al.—identified the genetic material i. wanted to know what substance was being transferred from the dead type S to the live type R 1. already knew that DNA, RNA, proteins, and carbs were major parts of living cells so they needed to separate them to determine if any of them were genetic material ii. prepared bacterial extracts from type S strains that contained each type of the above molecules iii. only the extracts with the purified DNA was able to convert the type R into type S iv. to prove that DNA extract was pure, they treated DNA extracts that digested RNA (RNase), DNA (DNase), and proteins (protease) 1. when treated with DNase it lost its ability to convert type R into type S therefore the transforming principle was DNA c. Experiment #3: Hershey & Chase—verified that DNA is the genetic material rather than protein i. studying T2 phage (no microelements)—a protein that destroys E-coli by injecting genetic material while virus heads stay on the outside 1. Phage reproductive cycle: a. Phage attaches to bacterial cell wall b. Phage injects DNA into host cell c. Expression of phage genes leads to the synthesis of phage components d. Phage components are assembled e. Host cell lyses and new phages are released ii. since T2 had DNA and protein, the genetic material needed to be one or the other so they radio labeled the protein (with 35S) and DNA (with 3P) iii. Process 35 32 1. Grow E. coli cells in media with S or 35 Inf32t T2 phage with them to produce new T2 phages labeled with S or P 2. Add 35S-labeled T2 phage into 1 flask and 3P-labeled T2 phage into the other. 3. Add uninfected E. coli cells to each flask 4. Agitate the solutions in blenders for different lengths of time to shear the empty phages off the bacterial cells 5. Centrifuge 6. The heavy bacterial cells will sink to the bottom while the lighter phag32 will stay on top 7. The P was found on the bottom in the bacterial cells, indicating that the genetic material was DNA instead of protein 3. Nucleic Acids a. Key terminology i. Nucleic acids = name for DNA and RNA because they are acidic therefore they release hydrogen ions in solution and have a net negative charge at neutral pH ii. Purines = 2 ring bases: adenine and guanine iii. Pyrimidines = 1 ring bases: thymine, cytosine, uracil iv. nucleotides = repeating structural unit of nucleic acids v. phosphodiester = linkage between nucleotides involves an ester bond between a phosphate group on one nucleotide and the sugar molecule on the adjacent nucleotide; the backbone vi. nucleoside = structure in which a base is attached to only a sugar vii. Chargraff’s rule = states that A pairs with T and C pairs with G via H bonds; by only bonding with certain things it keeps the width of the double helix constant (DNA with more G and C is more stable) viii. Base stacking = Bases form flattened regions which is favorable because the bases are nonpolar and can interact with each other; also stabilizes the double helix by excluding polar water molecules (aka bases are located within the double stand) ix. Grooves = indentations where the atoms of the bases are in contact with the surrounding water; some proteins can H bind to bases and affect conformation and function x. Major groove = wide indentation in the DNA double helix in which the bases have access to water xi. Minor groove = narrow indentation in the DNA double helix in which the bases have access to water xii. Depurination = rxn that removes a purine base (a/g) and gives rise to lesions xiii. Deamination = rxn in which there is a loss of an amino group from a cytosine in DNA which gives rise to a uracil b. General structure is made of 3 things: i. Central sugar ii. Phosphate groups attached to sugar iii. Nitrogenous bases c. RNA vs. DNA RNA DNA Exists as single stranded molecule Exists as double stranded molecule Sugar is ribose Sugar is deoxyribose Bases are ATCG Bases are AUCG Sunthesized in the 5’ to 3’ direction Synthesized in the 5’ to 3’ direction Many functions: regulatory, One function: storage molecule for the transcription, regulation of translation, “blueprint” of the body protein complex production d. 4 levels of complexity within the nucleic acid i. (1): nucleotides ii. (2): nucleotides are linked linearly via phosphodiester bonds to form 1 strand of DNA or RNA iii. (3): 2 strands of DNA interact with each other to form a double helix iv. (4): 3-D structure of DNA results from folding and bending of the double helix e. 3 components to a nucleotide i. 1 phosphate group attached to the 5’ carbon of the sugar ii. pentose sugar (OH group on the 3’ carbon is important in allowing nucleotides to form covalent linkages with each other) iii. nitrogenous base attached to the 1’ carbon of the sugar 4. Optical density of DNA a. Optical density—heat supernatant and watch how association and dissociation changes (more ATs will melt at lower temps therefore ppl could differentiate diff species and strains from this) b. Molecular hybridization—to reveal unique elements of DNA i. Concluded that microorganisms don’t have a lot of uniqueness (find homologs quickly) ii. Mammals and plants are unique and have a lot of repetitive units (takes a little longer for unique homologs to pair and less time for repetitive DNA to pair) 5. Repetitive DNA a. Transposition—jumping of a DNA segment to another place of the genome (2 types) i. DNA transposons = inactive in the human genome due to accumulation of mutations 1. How it functions: core of transposable element codes for an enzyme. Enzyme binds to ends of element. The ends of the transposon are formed by inverted repeats which can exchange DNA strands and stabilize stem-loop structure necessary for transposase action. Transposase cute transposon out and ligates resulting chromosomal DNA ends. ii. Retrotransposons = more abundant and still active in the human genome 1. How it functions: require RNA polymerases to transcribe them into RNA, whicle the original DNA copy stays in same location. 6. Watson-Crick model of DNA a. AT/CG Rule: i. A is complementary to T ii. C is complementary to G Ch. 13—DNA replication and recombination 7. Models of replication a. 3 models of replication i. conservative model = a hypothesis that states both DNA strands of parental DNA remain together following DNA replication ii. semiconservative model = a hypothesis that states that the ds DNA is half conserved following the replication process therefore the new ds DNA has 1 parent strand and 1 daughter strand 1. Experimental evidence: Meselson-Stahl and E.coli illustrated that DNA is semiconservative in bacteria 2. Experimental evidence: Alves and Jonasson illustrated that DNA is semiconservative in eukaryotes iii. dispersive model = hypothesis that states that segments of parental DNA and new DNA are interspersed in both strands following the replication process 8. circular DNA replication—E. coli a. key terminology i. ORI = site on the bacterial chromosome where DNA synthesis begins; synthesis of new daughter strands proceeds bidirectionally (~245 nucleotides long) ii. replication fork = the site where the parental DNA strands have separated and new daughter strands are being made (2 forks move in opposite directions outward from the origin) b. 3 DNA sequences found within the origin of replication i. AT-rich region—2 strands separate here ii. DnaA box sequences—serve as recognition sites for the binding of the DnaA proteins 1. Bind DnaA proteins to initiate the actual replication iii. GATC methylation sites—help regulate the replication process 9. Major players of replication Major player Function Addtnl Info Double stranded DNA To be unwound to provide the ss template strand Single-stranded binding Keeps the ss DNA from being proteins digested by binding and keeping the replication bubble open Helicase Unwinds the ds DNA molecule that sits at the top of the replication fork; breaks H bonds DNA polymerase Catalyzes the formation of - Has a 5’ to 3’ limitation covalent bonds between - RNA polymerase offers adjacent nucleotides to make a 3’ end for DNA new daughter strands polymerase to start adding dNTPs - DNA polymerase I excises RNA primers and fills in with DNA with deoxyribonucleoside triphosphates dNTPs - DNA polymerases II, IV, and V are involve in DNA repair - DNA polymerase III is responsible for most of DNA replication RNA primase Synthesizes an RNA primer for RNA polymerase Origin of replication Region of a specific - AT rich nucleotides that signals the beginning of transcription Replication fork The site where the leading and lagging strand separate Gryase (i.e. topoisomerase) Prevents the ds DNA from - Travels in front of supercoiling as it is being helicase unwound 10.Leading and Lagging strand a. Leading strand—continuous replication i. RNA primer is made at origin and DNA polymerase III adds nucleotides in the 5’ to 3’ direction sliding towards the fork b. Lagging strand—discontinuous replication i. Multiple RNA primers are made so that DNA polymerase III can add nucleotides in the 5’ to 3’ direction away from the fork ii. To complete okasaki fragments, RNA primers must be removed via DNA polymerase I, DNA must be made where the primers have been removed, and covalent attachement of adjacent fragments of DNA must happen iii. Process of DNA synthesis in the lagging strand 1. DNA strands separate at the origin and create 2 replication forks 2. Synthesis of the leading strand occurs in the same direction as the movement of the replication fork 3. The first okasaki fragment of the lagging strand is made in the opposite direction 4. The leading strand elongates 5. 2ndokasaki fragment is made 6. lrdding strand elongates st nd 7. 3 okasaki fragment is made and the 1 and 2 are connected together 11.Eukaryotic replication a. Key terminology i. Lesion-replicating polymerases = DNA polymerases that are attracted to damaged DNA and are able to synthesize the complementary strand over the abnormal region ii. Flap endonuclease = removes RNA primers iii. Telomere = the telomeric sequences within the DNA and the special proteins that are bound to these sequences (found at the end of linear chromosomes) iv. Telomerase = prevents chromosome shortening by recognizing the sequences at the ends of eukaryotic chromosomes and synthesizing additional repeats of telomeric sequences v. Proofreading = the mechanism by which DNA polymerase is able to remove mismatched bases b. General characteristics i. Have multiple origins of replication in which multiple groups of them are activated at the same time ii. Linear chromosomes therefore DNA replication occurs bi-directionally from the ORI during S phase iii. Genomes have multiple chromosomes iv. There is a larger DNA content than bacteria v. Many diff types of polymerase enzymes (see above) vi. Special process to replicate the chromosome ends via telomerases vii. Assembly of newly replicated DNA into nucleosomes viii. Replicates with high fidelity c. Replicating telomeres i. Problem: we have a 5’ to 3’ restriction. Can’t link together the first 2 individual nucleotides and it can only elongate only pre-existing strands. 3’ end of the linear chromosome can’t be replicated via DNA polymerase bc a primer can’t be made upstream therefore chromosome would become shorter with each round of DNA replication if the problem wasn’t solved ii. Solution: telomerase: part protein part RNA molecule w built in template that allows the generation of the chromosome ends 1. RNA part has a sequence complementary to DNA sequence in telomeric repeat to allow telomerase to bind to 3” overhang of telomere and synthesize nucleotides at end of DNA strand d. 3 characteristics of high fidelity replication i. H bonding between the appropriate bases are more stable than between mismatched pairs ii. Active site of DNA polymerase preferentially catalyzes attachment of nucleotides when the appropriate bases are across from each other iii. DNA polymerase enzymatically removes mismatched nucleotides Ch. 14—Gene transcription and modification 12.Central dogma of molecular biology a. DNA to mRNA to protein via replication, transcription, translation i. DNA replication makes DNA copies that are transmitted from cell to cell and parent to offspring ii. Transcription produces an RNA copy of a gene 1. mRNA is a temporary copy of a gene that contains information to make a polypeptide iii. translation produces a polypeptide using the information in mRNA iv. the polypeptide becomes part of a functional protein that contributes to an organism’s traits 13.Transcription a. Key terminology i. ribosome-binding site = the site for ribosome binding; translation starts near this site (ribosome scans mRNA for a start codon) ii. start codon = specifies the first AA in a polypeptide sequence, usually a Met in eukaryotes iii. stop codon = specifies the end of polypeptide synthesis iv. Regulatory sequences = site for the binding of regulatory proteins v. Regulatory proteins = influence the rate of transcription vi. Promoter = site for RNA polymerase binding; signals the beginning of transcription vii. Terminator = signals the end of transcription b. Major players i. RNA polymerase—moves along the DNA strand and causes it to unwind ii. DNA template (i.e. anti-sense strand)—used as a template for RNA synthesis iii. Ribonucleotides—RNA polymerase always connects them in the 5’ to 3’ direction c. 3 steps of transcription Step What’s happening Additional Info Initiation the promoter - promoters = the minimum functions as a DNA sequences needed for recognition site for basal transcription; promotes transcription factors gene expression (3 features which enable the found in most promoters) RNA polymerase to 1. transcriptional start site bind to the promoter; (core promotor) = short DNA following binding, the sequence necessary for DNA is denatured transcription to take place (3 into a bubble (i.e. the categories of proteins needed open complex) for basal transcription) RNA polymerase II— initiates transcription General transcription factors—needed for RNA polymerase II to initiate transcription of structural genes (e.g. mRNA) Mediator—mediates interactions between RNA polymerase II and regulatory transcription factors 2. regulatory elements = short DNA sequences that affect the ability of RNA polymerase to recognize the core promoter and begin transcription; recognized by transcription factors (2 categories) enhancers = activating DNA sequences involved with the alteration of the basal transcription rate (distal promoter element) silencers = DNA sequences that inhibit transcription 3. TATA box = proximal promoter element that determines the precise starting point for transcription Elongation RNA polymerase - Synthesis of the RNA transcript slides along the DNA 1. RNA polymerase slides along in an open complex to the DNA and creates an open synthesize the RNA complex as it moves 2. The DNA strand known as the template is used to make a complementary copy of RNA 3. RNA polymerase moves along the template strand in a 3’ to 5’ direction and RNA is made in the 5’ to 3’ direction using nucleoside triphosphates as precursors 4. U is substituted for T Termination a terminator is reached that causes RNA polymerase and the RNA transcript to dissociate from the DNA 14.RNA modifications a. Key terminology i. Exons = the coding sequences that are contained within mature RNA ii. Introns = intervening sequences = sequences found between exons that are removed from the genetic code iii. splicing = process that removes introns and stitches together exons in a mature RNA molecule iv. self-splicing = splicing that doesn’t require the aid of other catalysts v. spliceosome = multicomponent structure that recognizes the intron boundaries and properly removes it; splices pre-mRNA vi. alternative splicing = a possible advantage for a species to contain introns; states that when a pre-mRNA has multiple introns, variation may occur in the pattern of splicing to allow the resulting mRNAs to have alternative combos of exons (biological importance: 2 or more diff proteins can be made from a single gene to allow organism to carry fewer genes in genome b. Modifications Modification Description Occurrence Processing The cleavage of a large RNA Occurs in both prokaryotes transcript into smaller pieces; and eukaryotes and happens 1+ smaller pieces becomes a for rRNA and tRNA functional RNA molecule Splicing Involves cleavage and joining Common among eukaryotic of the RNA molecule; pre-mRNAs, sometimes in removes introns and stitches rRNAs, sometimes in tRNAs, together exons and rarely in bacterial RNAs 5’ capping The attachment of a Eukaryotic mRNAs; occurs methylguanosine cap to the 5’ while the pre-mRNA is still end of an mRNA; plays key being made by RNA role in splicing of introns, exit polymerase II of mRNA from nucleus, and binding of mRNA to ribosome. Functions: allows mRNAs to exit nucleus, allows for early translation, allows for efficient splicing of introns 3’ poly-A-tailing The attachment of a string of Eukaryotic mRNAs and some adenine-containing bacterial RNAs nucleotides to the 3’ end of mRNA at a site where the mRNA is cleaved; important for stability and translation; important for stability so the mRNA can leave the nucleus RNA editing—a change in the The change of the base Some eukaryotic RNAs nucleotide sequence of an sequence of an RNA after it RNA molecule that involves has been transcribed; can additions or deletions of generate start codons, stop certain bases or conversions codons, and change the of 1 base into another coding sequence for polypeptide Base modification Covalent modification of a Common in tRNAs base within an RNA molecule 15.RNA types a. Messenger RNA—mRNA i. Encodes the sequence of AA within a polypeptide ii. Transcribed by RNA polymerase II iii. Modified by polyadenylation = cleavage near their 3’ end and attachment of a string of adenine nucleotides iv. Pre-mRNA = the long transcript produced by the transcription of structural genes within nucleus; usually altered by splicing and other modifications before it can exit the nucleus and start to become mature b. Ribosomal RNA—rRNA i. Necessary for the translation of mRNA; make up ribosomes and protein subunits ii. Transcribed by RNA polymerase I c. Transfer RNA—tRNA i. Necessary for the translation of mRNA ii. Transcribed by RNA polymerase III iii. Requires processing via endonucleases and exonucleases 1. Exonuclease = cleaves a covalent bond between 2 nucleotides at one end of a strand 2. Endonuclease = cleaves the bond between 2 adjacent nucleotides 3. Made as large pre-cursors that have to be cleaved to produce mature and functional tRNAs d. microRNA i. short RNA molecules involved in gene regulation e. scRNA—small cytoplasmic RNA i. found in the cytoplasms and is necessary to target proteins to the ER ii. component of the signal recognition particle (SRP) f. RNA of RNaseP i. Catalytic component that is necessary in the processing of bacterial tRNA ii. Ribozyme = RNA molecule with catalytic activity g. snRNA—small nuclear RNA i. necessary in the splicing of eukaryotic pre-mRNA ii. snRNAs and proteins combine to form small nuclear riboproteins (snRNPs) that are components of the spliceosome iii. transcribed by RNA polymerase II h. telomerase RNA i. enzyme telomerase is made of an RNA molecule and protein subunits i. snoRNA—small nucleolar RNA i. necessary in the processing of eukaryotic rRNA transcripts 16.The genetic code a. Key terminology i. sense codons = the sequence of 3 bases in most codons that specifies a particular AA ii. start codon = AUG codes for Met; the first codon that begins a polypeptide sequence iii. reading frame = defined by the start codon; a sequence of codons determined by reading bases in groups of 3 beginning with the start codon iv. frameshift mutation = mutation in which a single-nucleotide insertion would alter the reading frame beyond the point of insertion and destroy proper protein function thereafter v. stop codons = non-sense codons = termination codons = UAA, UAG, UGA; used to end the process of translation b. Characteristics i. 3-letter code referred to as a codon ii. linear iii. co-linear—describes the 1 to 1 correspondence between the sequence of codons in the DNA-codoing strand and the AA sequence of the polypeptide iv. universal v. redundant or degenerate vi. unambiguous c. Wobble hypothesis i. States that the 1 and 2 ndcodon positions are more important in attracting rd correct tRNA than the 3 position 1. The anticodon of a single form of tRNA can pair with more than 1 codon in mRNA ii. Occasionally we can have mismatches btwn tRNA and codon iii. Wobble rules = state that the first 2 positions of the codon pair strictly to the AU/GC rule but the third position can tolerate certain types of rd mismatches therefore the base at the 3 position doesn’t have to H bond as precisely with the corresponding base in the anticodon; enables a single tRNA to recognize more than one codon iv. Isoacceptor tRNAs = when 2 or more tRNAs that differ at the wobble base are able to recognize the same codon Ch. 15—Translation of mRNA 17.The polypeptide a. Key terminology i. Peptide bond = formed as a polypeptide is made between the carboxyl group in the last AA of the polypeptide and the amino group in the AA being added ii. N-terminus = the end at which the first AA is located at; amino group found here iii. C-terminus = the end at which the last AA is located; carboxyl group found here iv. R-group = side chain = each AA contains this with particular chemical properties 18.AA structure a. Major properties i. Size ii. Charge iii. Hydrophilic/hydrophobic—play important role in dictating the shape 1. Hydrophobic AA are buried within the interior of a folded protein 2. Hydrophilic AA are more likely to be on the surface of a protein where they can favorably interact with water b. Hierarchies of folding i. Primary—linear ii. Secondary—a regular, repeating shape; stabilized by the formation of H bonds between atoms in the polypeptide backbone 1. Alpha helix 2. Beta sheet (alpha or beta) a. Parallel b. Antiparallel iii. Tertiary—3D structure of proteins that arise from secondary structures folding into each other iv. Quaternary—made of 2 or more polypeptides that associate with each other to make a functional protein (e.g. hemoglobin) 19.Translation a. Key terminology i. Ribosomes = the macromolecular arena where translation occurs (contains a large and small subunit that act as adaptors to bring the AA close enough so that a covalent bond can form between them) ii. rRNA = ribosomal RNA = constitutes the mass of the ribosome iii. adaptor hypothesis = hypothesis by Crick that states that the position of an AA within a polypeptide is determined by the binding between the mRNA and an adaptor molecule (tRNA) carrying a specific AA iv. anticodons = 3-nucleotide sequences that are complementary to codons in mRNA b. 3 key sites on the ribosome i. A site = site that you go to when you want to add an AA to a growing peptide chain ii. P site = site you go to after the A site where the AA is linked to the peptide chain iii. E site = site where the spent tRNA is moved by the large ribosomal subunit c. tRNA i. Overview 1. tRNA molecules carry the AA that correspond to the codons in the mRNA so the order of codons in mRNA dictates the order of AA within 2. codons in mRNA are recognized by the anticodons in tRNA ii. General structural features 1. cloverleaf pattern a. 3 stem loops b. few locations with additional nucleotides not found in all tRNA molecules c. acceptor stem with a 3’ ss region iii. Aminoacytl tRNA-synthetase—enzyme that catalyzes the attachment of the AA to tRNA molecules 1. Rxn process: synthetase recognizes AA and ATP. ATP is hydrolyzed resulting in the attachment of AMP to the AA and the release of pyrophosphate. Correct tRNA binds to the synthetase. AA becomes covalently attached to 3’ end of the tRNA molecule at acceptor stem. AMP is released. Charged tRNA = aminoacyl tRNA = results dur to the realease from aminoacyl tRNA synthetase d. 3 general stages i. initiation 1. ribosomal subunits, mRNA, and the first tRNA assemble to form a complex. Ribosome slides along mRNA moving over the codons 2. initiator tRNA = specific tRNA that recognizes the start codon in the mRNA ii. elongation 1. Ribosome slides along mRNA moving over the codons a. As ribosome moves the tRNA molecules bind to mRNA in the ribosome and bring them the right AA 2. tRNAs bring the first AA to the A site and a series of peptidyl transferase reactions create a polypeptide a. at each step, the polypeptide is transferred from the A site to the P site and are released from the E site iii. Termination 1. Occurs when a stop codon is reached. Disassembly occurs and the newly made polypeptide is released 2. Release factor binds to a stop codon in the A site which promotes the cleavage of the polypeptide from the tRNA and the subsequent disassembly of the tRNA. mRNA, and ribosomal subunits Ch. 18—Gene mutation and DNA repair 20.Types of mutations a. Key terminology i. Gene mutation = occurs when the sequence of the DNA within a gene is altered in a permanent way; relatively small change in DNA structure that affects a single gene ii. Wild-type = a relatively prevalent genotype iii. Mutant allele = an allele that arose from the mutation of the wild-type gene iv. Reversion = the process in which a reverse mutation occurs and changes the mutant allele back to a wild-type allele v. Conditional mutations = some mutation that affect the phenotype only under a defined set of conditions b. Mutations in the coding regions of genes Mutation type Definition Addtnl Info Point mutation A change in a single Three classifications of point mutations base pair within the 1. Substitution—replacing one letter DNA with another AA substitution?: will see some consequences, however, if we replace a hydrophobic AA with another hydrophobic AA, we won’t see a big change if at all 2. Deletion—omitting a nucleotide from the sequence, creating a frameshift 3. Insertion—adding 1 more nucleotide, creating a frameshift Transition A change of a - More common than transversions pyrimidine to another pyrimidine (i.e. C to T) or a purine to another purine (i.e. G to A) Transversion A change of a purine to a pyrimidine Silent mutations Mutations that don’t - Can occur because the genetic alter the AA sequence code is degenerate of the polypeptide even though the nucleotide sequence has been changed Missense mutations Base substitutions in - Ex = sickle cell anemia; mutation which an AA change in the beta-globin gene that alters th does occur the polypeptide sequence so the 6 AA is changed from glutamic acid to valine - Neutral mutation = results from a missense mutation that has no detectable effect on protein function Nonsense mutations Mutations that involve - Terminates the translation of the a change from a polypeptide earlier than expected normal codon to a stop - Can inhibit the expression of codon downstream genes (i.e. polarity) Frameshift mutations Mutations that involve - Results in a completely different the addition or deletion AA sequence downstream from the of a number of mutation nucleotides that is not divisible by 3 c. Mutations in the noncoding sequences of genes—affecting gene expression Mutation type Definition Addtnl Info Up-promoter mutations A mutation that - Make a sequence more like the increases the cconsensus sequence transcription rate Down promotor A mutation that - Makes the promoter to become mutations decreases the less like the consensus sequence transcription rate because it decreases the promoter’s affinity for transcriptions factors Deleterious mutation A mutation that - Lethal mutation = mutation that decreases the chances results in death to the organism of survival and - Beneficial mutation = mutation reproduction that enhances the survival or reproductive success of an organism Suppressor mutations Second-site mutations - Occurs at a DNA site that is that suppresses the distinct from the first mutation phenotypic effects of - Classified according to relative another mutation locations in regard to mutation they suppress - Intragenic suppressor = suppresses the effect of an earlier mutation within the same gene involves a change in protein structure - Intergenic suppressor = suppresses the effect of an earlier mutation in another gene; involves a change in the expression of 1 gene that compensates for loss-of- function mutation affecting another gene Loss of function mutation Mutation that causes a complete or partial loss of protein function Gain of function mutation Mutation that causes the appearance of a new trait or protein function; also causes the appearance of a trait within inappropriate places d. Chromosomal structure mutations—rearrangements Rearrangement Additional info Deletion (2 types)—change in total amt of - occurs when a segment of DNA chromosomal material is missing 1. terminal deletion = deletion in which - cause of misalignment: chromosome a chromosome breaks into 2 and the carries 2 or more similar DNA piece without the centromere is lost sequence and degraded 2. interstitial deletion = deletion in which the chromosome breaks in 2 places and the central fragment is lost Duplication—change in the total amount of - a section of the chromosome is DNA repeated compared to the normal parent - Ohno’s hypothesis = states that duplications are essential for evolution bc they lead to gene families Inversion—chromosomal rearrangement, 2 - Change in the direction of the genetic types: material along chromosome 1. Pericentric = inversion in which the centromere is within the inverted region 2. Paracentric = inversion in which the centromere is outside the inverted region Simple translocation—chromosomal - a single piece of the chromosome is rearrangement attached to another chromosome Reciprocal translocation - 2 diff chromosome types exchange pieces to make 2 abnormal chromosomes - i. Whole genome changes (i.e. large scale whole chromosome changes)—2 1. Variations in the number of sets of chromosomes a. Polyploidy = phenomenon in which the organism contains 3 or more sets of chromosomes (e.g. triploid/tetraploid/etc.) b. Endopolyploidy = the occurrence of polyploid tissues/cells that are otherwise diploid (e.g. liver cells. Biological implication: increase in chromosome set number may enhance cells ability to produce specific gene products needed in abundance) 2. Variations in the number of specific chromosomes within a set a. Aneuploidy = an alteration in the number of particular chromosomes therefore the total number of chromosomes isn’t an exact multiple of a set i. Trisomy = 1 extra chromosome (2n+1) with a genetic imbalance of 50% more gene expression ii. Monosomy = 1 less chromosome (2n – 1) with a genetic imbalance of 50% less gene expression 21.Germ-line and Somatic mutations a. Key terminology i. Germ line = cells that give rise to gametes (egg and sperm) ii. Somatic cells = comprise all cells of the body exclusing germline cells iii. Genetic mosaic = an individual that has somatic regions that are genotypically different from each other b. Germline vs. Somatic mutation Germ line Somatic Important for evolution because these Mutations can happen during late or early mutations result in major phenotypic stages of development— consequences therefore the offspring could thrive or die Can occur directly in a sperm or egg cell or in Size of the affected region depends on the a precursor cell timing of the mutation Mutation will be found throughout entire Mutation is only found in the affected area— body can result in genetic mosaics Half of the gametes will carry the mutation None of the gametes will carry the mutation 22.Spontaneous mutations a. Key terminology i. Spontaneous mutations = changes in DNA structure that result from natural biological or chemical processes ii. Depurination = process in which a purine (i.e. A or G) is removed from the DNA iii. Deamination = spontaneous lesion in which an amino group is removed from the cytosine base and produces uracil iv. Tautomeric shift = forms of bases can interconvert by a chemical reaction that involves the migration of a H atom and a switch of a single bond and an adjacent double bond; occurs prior to DNA replication v. Oxidative stress = an imbalance between the production of a reactive oxygen species and an organism’s ability to break them down vi. Reactive oxygen species = ROS = products of oxygen metabolism in all aerobic organisms (e.g. hydrogen peroxide, superoxide, hydroxyl radical) vii. Oxidative DNA damage = changes in DNA structure that are caused by ROS b. Causes of spontaneous mutations Cause Description Aberrant recombination Abnormal crossing over may cause deletions, duplications, translocations, and inversions Aberrant segregation Abnormal chromosomal segregation can cause aneuploidy or polyploidy Errors in DNA replication Mistake by DNA polymerase can cause a point mutation Transposable elements Can insert themselves into the sequence of a gene Depurination Linkage between purines and deoxyribose can break and not be repaired Deamination Cytosine and 5-methylcytosine can deaminate to create uracil or thymine Tautomeric shifts Changes in base structure can cause mutations if they occur immediately prior to DNA replication Toxic metabolic products Products of metabolic processes can be chemically reactive agents that alter DNA structure 23.Induced mutations a. Key terminology i. Induced mutations = changes in DNA structure that are caused by environmental agens ii. Mutagens = agens known to alter the structure of DNA which lead to mutations iii. Mutation rate = the likelihood that a gene wil be altered by a new mutation b. Causes of induced mutations Cause Description Chemical agents - Chemical substances can cause changes in DNA structure: photon interacting with electron, electron interacting with water molecules in the cell, polarity causes more charged Hs, dose increases Nitrous acid - Deaminates bases by changing the amino group to a keto group (NH2 → =O) Nitrogen mustard - Alkylates bases—disrupt pairing by adding an ethyl or a methyl to the base Ethyl methanesulfonate - Akylates bases Proflavin - Directly interferes with the DNA replication process by inserting itself between adjacent base pairs to distort the helix; single nucleotide addition or deletions can occur to create a frameshift mutation 5-bromouracil - A base analog that becomes incorporated into daughter strands during replication (thymine analog) - Used in chemotherapy bc it inserts themselves into the DNA of actively dividing cancer cells which will lead to the death of them 2-aminopurine - Base analog Physical agents - UV light and X-rays can damage DNA: displace nucleotides and result in gaps - Classic paradigm of radiation injury X-rays - Cause base deletions, ss DNA nicks, crosslinking, and chromosomal breaks UV light - Promotes pyrimidine dimer formation (e.g. thymine dimers) - Thymine dimers interfere with transcription and DNA replication 24.How we can determine whether a chemical is mutagenic: Ames test a. Key terminology i. Ames test = a test that uses strains of a bacterium that cant synthesize histidine. b. Ames test process: i. Overall: a testing method that monitors whether an agent increases the mutation rate 1. Suspected mutagen is mixed with rat liver extract and a strain of bacteria that cant synthesize histidine (mutagen may need activation by cell enzymes provided by rat liver extract) 2. Bacteria plated on growth medium without histidine (bacteria not expected to grow on these plates but if a mutation occurs that allows it to synthesize histidine, it can grow) 3. Mutation rate is estimated by counting the grown colonies on the media and compared with the number of bacterial cells that were originally streaked on the plate 25.DNA repair a. DNA repair systems DNA Repair System Description Direct repair Enzyme recognizes an alteration in DNA structure and converts it back to its correct structure Base excision repair and nucleotide excision Abnormal base/nucleotide is 1 recognized repair and removed from DNA, a segment of DNA in the region is removed, and complementary DNA strand is used as template to synthesize normal DNA strand Mismatch repair DNA defect is base pair mismatch that is recognized and a segment of DNA in the region is removed. Parental strand is used to synthesize normal daughter strand Homologous recombination repair Occurs at ds breaks or when DNA damage causes a gap in synthesis during DNA replication. Strands of normal sister chromatid are used to repair damaged sister chromatid Nonhomologous end joining Occurs at ds breaks. Broken ends are recognized by proteins that keep the ends together and the broken ends are re-joined 26.Transposable elements a. Overall: transposable elements can disable a gene, disrupt translation of a gene, or have no effect by inserting itself into an intron; influence is dependent on the specific transposon
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