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by: Kennedy Finister


Marketplace > Auburn University > BIOL3000 > GENETICS EXAM 3 STUDY GUIDE
Kennedy Finister
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chapters 9- 13.2 DNA replication/recombination Transcription and RNA processing Translation Control Of Gene expression Mutations
Rita Graze
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Genetics, biol 3000, Auburn University, Study Guide, Biology, Exam 3, rita graze
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This 12 page Study Guide was uploaded by Kennedy Finister on Thursday April 14, 2016. The Study Guide belongs to BIOL3000 at Auburn University taught by Rita Graze in Fall 2015. Since its upload, it has received 20 views.




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Date Created: 04/14/16
Exam 3 Study Guide 1. Know the molecular definition of a gene? All the DNA sequence necessary to synthesize a functional molecule and/or protein 2. Know the basic steps of transcription. Describe what happens at each step. Basic Steps: 1. Recognition of the core promoter, binding of TFIID (TBP), TFIIA, and TFIIB recruits RNAPII 2. Initiation- Binding of RNAPII complexed with TFs, mediator complex + more = the holoenzyme. Interactions between holoenzyme and activators (specific TFs) in regulatory regions trigger initiation (change in protein conformation) - release from the promoter. CTD Tail phosphorylation is involved in initiation. 3. Elongation- Elongation factors added = RNA pol II moves along the DNA transcribing the RNA molecule. CTD Tail phosphorylation is involved in elongation. 4. Termination- STOP, RNAPII releases DNA, signal is GC rich regions + cleavage of transcript 1. Recognition- TBP- TATA Binding Protein, essential component of TFIID recognizes and binds to the TATA box. TFIID Complex - forms at the promoter and recruits other general transcription factors that are required for recognition of the promoter by RNA polymerase II. A. TBP attaches to the minor gr oove, inserting amino acid side chains between the bases. This is stabilized by H -bonds, it actually distorts the DNA, causing it to bend. 2. Initiation- Binds to the BRE site recruits to RNAPII at the INR and DPE. Specific transcription factors bound to distant enhancers and to the proximal regulatory region. a. RNA polymerase Holoenzyme - basal transcription apparatus 3. Elongation- The RNAPII complex opens the bubble ahead of itself and closes it behind. The Elongation Factors evict the histones ahead of RNAPII and replace them behind it. Maintain heteroduplex RNA: DNA hybrid region; deals with speed bumps. 4. Termination- Involves GC rich regions at the 3’ end of the gene. Involves cleavage of the RNA and 3’ processing of the transcript. Dephosphorylation of the R NA Polymerase II. 3. Be able to match different types of RNA (for example tRNA) to definitions or steps of molecular processes mRNA- Carries genetic code (processed form) hnRNA- heterogeneous RNA, pre mRNA rRNA- ribosome function (part of the ri bonucleoprotein complex) tRNA- transports amino acids snRNA- small nuclear RNA- processing of hnRNA snoRNA- small nucleolar RNA- assembly of rRNA miRNA- micro RNA- regulates stability and translation of mRNA siRNA- small interfering RNA- similar to micro RNA, also antiviral 4. Know 3 major differences between an mRNA and a pre -mRNA and the functions of these modifications. Messenger RNA carries the coding instructions for polypeptide hains from DNA to the ribosome. After attaching to a ribosome, an mRNA molecule specifies the sequence of amino acids in a polypeptide chain and provides a template for joining amino acids. Larger precursor molecules, pre -messenger RNA, are the intermediate products of transcription in eukaryotic cells. Pre -mRNAs also called primary transcripts, are modified extensively before becoming an mRNA and exiting the nucleus for translation into protein. Bacterial cells do not possess pre -mRNA in these cells; transcription takes place concurrently with translation. 5. Be able to match the 2 unusual phosphodiester bonds that form during mRNA processing to steps of the process and figures showing these bonds. Page 273 when introns and exons are spliced and the intron is released as th e lariat. 6. Basic Amino Acid structure. 7. The genetic code; how many possible codons, how many standard AAs, how many bases in a codon etc. There are 20 standard amino acids and 64 possible codons. There are 3 nucleotides or bases in each codon . Groups of codons that code for the same AA are called synonymous • Universal- rare exceptions (different termination codons) o Natural: asterix= sometim es not used, red= noncanonical o Artificial: reassign a stop codon Features of Genetic code: • Written in a linear form (stored in the mRNA) • Coded as triplets (codons) • Unambiguous- (A codon= a single amino acid) • Degenerate (1 AA can be coded for by more th an 1 codon) more info than needed 61 codons= 20 AAs • Specific start and stop codons (START - AUG, GUG, UUG, CUG) (STOP - UAA, UGA, UAG) • There are 61 sense codons - meaning the codons that code for amino acids and not stop or start • Comma-less (there are no pauses in the code) 8. Know what wobble is, what property of the genetic code is it related to and why? Wobble is the idea that more than one base pair combination in a codon can result in the production of the same amino acid. Wobble base pairs are fundamental in secondary RNA structure and are critical for the proper translation of the genetic code. Wobble explains degenerate code. Because there are 61 sense codons and only 20 different amino acids commonly found in proteins, the code contains more information than is needed to specify the amino acids. 9. Types of R groups (positive charge, negative cha rge, hydrophobic and hydrophilic) and their properties (you don’t need to memorize all the amino acids that are polar etc.) Know that these can affect properties of the protein like overall charge and position of side chains within tertiary structure. Non-Polar- hydrophobic- repels water Polar- hydrophilic- attracts water Positive charge- Negative charge- Tertiary structure depicted by ribbon structure. Polar hydrophilic groups on outside and nonpolar hydrophobic groups on the inside. Chain of AA is b eing modified and combined side chains confer a particular function to protein. If you change an AA in that protein you might change the function of the protein. 10. Know the different ways that proteins can be post -transcriptionally modified. 1. Capping and Methylation 2. Modification of the 3’ End: Addition of a poly-A tail (3’ end) 3. Cleavage and Polyadenylation 4. Modification of the Middle: SPLICING a. Exons: Protein coding=phenotype. b. Introns: “Intervening Sequences”, areas of genes that do not generally code for phenotype c. Splicing: removal of intronic sequences, the spliceosome is the large complex of proteins and RNAs which excise introns in the nucleus of the cell 11. Know what primary, secondary, tertiary, and quaternary structures are. Primary- sequence of amino acids in the peptide. Secondary Structure- the interaction between amino acids and the configuration in space. • The spiral of amino acids is held together by hydrogen bonds. • This can form coils of coils and the sidechains stick outwards. • Can be parallel or anti-parallel • Hydrogen bonds between the NH and CO groups hold the sheet together • Alpha helix or Beta sheet Tertiary- conformation, overall shape, and 3 D figure • 3D structure that is specific to a certain protein • Polar hydrophilic groups are on the surface • Non-polar hydrophobic groups are on the inside • Folding can be spontaneous or aided by protein chaperones Quaternary- association of multiple peptides to form a functional protein • Protein function results from shape and the chemical properties of the amino acids • Shape is determined by amino acid sequence 12. Know about Alpha helixes and beta sheets and how they are held together The alpha helix is held together by hydrogen bonds between the molecules of the peptide bond and another molecule. The beta sheet held together by hydrogen bonds but generally only areas that contain large amounts of the amino acid glycine like to form these sheets. 13. Know the differences between prokaryotic and eukaryotic genes and prokaryotic and eukaryotic regulation. Prokaryotes • Prokaryotic mRNA is not processed before translation. • Translation of prokaryotic mRNA can begin before transcription is complete • TRANSCRIPTION IS THE KEY STEP BY WHICH PROKARYOTES REGULATE GENE EXPRESSION • Prokaryotic genes are organized into operons • No introns • Regulatory regions (operators) are between the promoter and coding region • Transcription unit contains multiple genes --- polycistronic RNA • The TRP operon: • TRP OPERON Eukaryotes • Enhanced I can stimulate the transcription of Gene A but its effect on Gene B is blocked by the insulator • Enhancer II can stimulate the transcription of Gene B but its effect on Gene A is blocked by the insulator. 14. Know the difference between genes (in prokaryotes) that are classified as negative inducible, negative repressible, positive inducible, positive repressible. Note negative means the regulator is the repressor, positive means it’s the activator, inducible means the default state is “O FF” and repressible means the defaults state is “ON” Positive Inducible- transcription is normally off (the activator is usually inactive) but the substrate make the activator active and turns transcription back on. (substrate present=gene expression) E x. Genes req for maltose metabolism Negative Inducible- transcription is normally off (repressor is normally active) definition of inducible. Def of negative —regulator is a repressor. • No substrate= no gene expression • AN inducer binds to a repressor result ing in a change in shape (that causes it NOT to bind to DNA) • The repressor is allosteric (changes shape) Negative Inducible diagram Positive Repressible- (positive meaning there is an activator) and repressible meaning that transcription is normally on (the activator is normally active) • Product present= no gene expression Positive Repressible Diagram: Negative Repressible Gene Expression - (negative meaning there is a repressor) repressible meaning transcription is normally on (the repressor is nor mally inactive) • Example: TRP operon • Product present= no gene expression Negative Repressible Gene Expression Diagram (red circled item also called the co -repressor) 15. Know the levels at which a genes expression can be regulated and mechanisms for regulation at each level. 1. At Transcription: ON at some rate/ OFF; subje ct to influence by internal or external cellular environment. 2. Post Transcriptional: Message stability/degradation; cap and tail addition - changes the amount of time an mRNA can be use d a. Can involve RNA splicing, RNA Degradation, Poly(A) tails, Cap removal, localization, and RNA interference 3. Translational: Where/when the mRNA is used to make protein a. There are different regulatory mechanisms that can regulate translation such as RNA interference 4. Post-Translational: Modifications made to the protein product (lipid, sugar, methyl, acetyl, phosphate); protein stability; protein activity/conformation - determines the localization and function of protein in the cell. 16. Enhancer, Silence rs and Insulators in regulatory regions (what they do at a basic level) 2a. Enhancers and Insulators: a. Enhancers enhance transcription rates b. Insulators- boundary sequences that block or insulate promoters from the effects of enhancers or silencers c. Silencers: reduce transcription rates (sometimes at same site) 17. Know the difference between general specific transcription factors a. Specific Activators/ Transcription Factors: Stabilize the holoenzyme, sometimes chromatin modification, specific for d ifferent genes (regulatory) b. Specific Transcription Factors: bound to distant enhancers and to the proximal regulatory region c. General Transcription Factors: Required for all transcription in all genes 18. Answer questions about tissues specific expressi on, given basic examples of genes and pathways. • Regulation is important to the differentiated state of cells and the tissues they make up • Genes give tissues their differentiated properties o Differentiated- specialized § NON dividing- have left the cell cycle G (0) • No telomerase activity  She will probably ask the cone and rods question o Rods- more of these and more sensitive to light, night vision § Rod cells- only one type expresses rhodopsin (an opsin is a light receptor protein) o Cones- color vision § Cone Cells- of three different types express different photosp ins which respond to different wavelengths of light  Expression and Differentiation: 1. Precursor cells in the eye differentiate into rod or cone cells 2. That means expressing the right genes (rhodospins for ro d cells) and not expressing the wrong ones ♦ Regulation is required both for the process of differentiation and for correct expression in cell type. 19. Know that RNAs have a lifespan that can be regulated by regions in the 5’ and 3’ UTRs and different me chanisms, which result in degradation of the transcript. Gene Regulation by RNA processing and Degradation: d. Gene Regulation Through RNA Splicing- alternative splicing allows a pre - MRNA to be spliced in multiple way s, generating different protein s in different tissues or at different times of development. The regulation of splicing is important in controlling gene expression. e. The Degradation of RNA - The amount of protein that is synthesized depends on the amount of corresponding mRNA available fo r translation. The amount of available mRNA depends on both the rate of mRNA synthesis and the rate of mRNA degradation. i. 5’ cap and poly-a tail- page 325 continued. ii. P bodies- iii. Sequences in 5’ untranslated region iv. Sequences in 3’ UTR 20. Know that translation can be blocked either by directly preventing initiation of translation or indirectly via regulation of the location of the RNA molecule. 21. RNA interference involves both exogenous and endogenous dsRNAs, be able to identify some examples of each Exogenous RNA- can also be processed Foreign dsRNA triggers silencing of viral genes as part of aniviral defense Endogenous- dsRNAs (miRNAs, endosiRNAs and more) are part of gene regulation Example: viral RNA- virus infection of the cell can generate dsRNA, RNA interference, destroys the viral RNA, preventing the formation of the new virus Example: The worm discovered by Fire and Mello: sense RNA, antisense RNA, Double stranded RNA. Double Stranded was only affected. 22. Know the roles of dicer and RISC complex in the RNA interference pathway dicer- removes the loop leaving the stem RISC complex- regulates the expression of genes complementary to part of the ssRNA 23. Know the possible regulatory effects of miRNAs and siRNAs a. RNA Cleavage- RISCs that contain siRNA and some that contain miRNA, pair with mRNA molecules and cleave the mRNA near the middle of the bound siRNA. This cleavage is carried out by a protein called slicer. After cleavage, the mRNA is further degraded. Thusm the presence of siRNAs and mirRNAs increases the rate at which miRNas are broken down and decreases the amount of protein produced. b. Inhibition of Translation- Some miRNAs regulate genes by inhibiting the translation of their complementary mRNAs. This can inhibit translation. c. Transcriptional Silencing- other siRNas silence transcription by altering chromatin structure. These siRNas combine with proteins to form a complex called RITS (for RNA transcriptional silencing), which is analogous to RISC. The siRNA component of a RITS then binds to its complementary sequence in DNA or an RNA molecule in the process of being transcribed and represses transcription by attracting enzymes that methylate the tails of histone proteins. The addition of methyl groups to t he histones causes them to bind DNA more tightly, restricting the access of proteins and enzymes necessary to carry out transcription. 24. The mutation vocabulary in table 13.2 25. What happens when mutations are somatic vs when they occur in germ line Somatic mutations: 1. occur in non-reproductive cells 2. And are passes to new cells through mitosis, creating a clone of cells having the mutant gene Germ Line Mutations: 1. Occur in cells that give rise to gametes 2. Meiosis and sexual reproduction allow germ-line mutations to be passed to approximately half the members of the next generation …. 3. …..Who will carry the mutation in all their cells 26. Know the 2 major classes of mutations (spontaneous and induced) and the about different causes (ex. Replication errors, chemical changes, intercalating agents, chemical exposure, free radicals, and UV light) 1. Spontaneous a. Causes: i. Nothing, natural, for example low DNA polymerase fidelity, No artificial factors or external regulators that cause the mutation to occur ii. Abnormal crossing over - including homologous and nonhomologous crossover iii. Replication Errors 1. Repeat expansions 2. Anomalous base-pairing a. Rare bases 3. Spontaneous Chemical Changes a. Depurination b. Deamination c. Base Analogs 2. Induced: Mutations caused or induced by external factors (mutagens), usually chemical or environmental, which cause a nucleotide change a. Causes: i. Chemicals that interact with DNA including 1. Artificial deamination 2. Base analogs 3. Intercalating agents ii. Radiation- Radioactive isotopes, X-rays, and UV 1. Direct 2. Free Radicals


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