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Genetics Exam 3 Study Guide

by: Jessica Brown

Genetics Exam 3 Study Guide BSCI - 30156 - 002

Jessica Brown

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About this Document

Study Guide using material from the book and lecture
Chi-hua Groff (P)
Study Guide
Genetics, Science
50 ?





Popular in Biological Sciences

This 8 page Study Guide was uploaded by Jessica Brown on Monday April 11, 2016. The Study Guide belongs to BSCI - 30156 - 002 at Kent State University taught by Chi-hua Groff (P) in Fall 2015. Since its upload, it has received 41 views. For similar materials see ELEMENTS OF GENETICS in Biological Sciences at Kent State University.


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Date Created: 04/11/16
Genetics Exam 3 Study Guide Highlight: definition Highlight: question Highlight: important information DNA Replication DNA Replication: genetic material is transmitted from parent to offspring and from cell to cell, for this to occur genetic material must be copied  DNA is a double helix o Two strands are held together in the helix by hydrogen bonds o The strands have an antiparallel alignment  During DNA replication the two strands separate o One becomes the template strand and one becomes the parental strand o The two new strands are the daughter strands  DNA replication is semiconservative o This means that the double stranded DNA is half conserved following the replication process  This means the newly made double stranded DNA contains one parental strand and one daughter strand  Origin of Replication: This is where DNA synthesis begins o Bacterial chromosomes have one origin of replication  The synthesis in bacteria occurs bidirectionally  Replication Fork: Where the parental DNA strands have separated and new daughter strands are being made o In bacteria the two replication forks move in opposite directions  DNA replication is initiated by DnaA proteins binding to sequences in the origin known as DnaA box sequences o DnaA Box Sequences: a recognition site for the binding of DnaA proteins o DNA Helicase: breaks hydrogen bonds between two strands of DNA o DNA Primase: Synthesizes an RNA primer  The primase allows the polymerases to start synthesizing the daughter strands  RNA Primer is placed at the origin of the leading strand  RNA primers are removed and the DNA fragments must be joined to form a continuous strand and complete replication o DNA Ligase: covalently links the okazaki (DNA) fragments together o DNA Polymerase 1: excises the RNA primers and fills in with DNA  Removes RNA fragments o DNA Polymerase 3: synthesizes a daughter strand of DNA  Conducts a majority of replication  DNA polyermases attach new nucleotides in the 5’ to 3’ direction  DNA Polymerases require shorter strands of RNA  In the lagging strand replication occurs away from the replication fork but it is still in the 5’ to 3’ direction o Only short fragments of nucleotides are attached at one time (1,000- 2,000) o Each fragment will contain a short RNA primer at the 5’ end  These fragments are known as okazaki fragments Homologous Recombination  Recall recombination from the last exam o Creates genetic diversity o Separates mutations that can have severely deleterious effects and brings together combinations of mutations that when combined can be beneficial  Genetic recombination: the process in which chromosomes are broken and rejoined to form new genetic material o Homologous recombination occurs between genetically similar sequences  Holliday proposed the mechanism to explain the molecular steps of homologous recombination o This is known as the Holliday Model  Illustrated in figure 13.24a  Holliday Junction: formation of a covalent linkage  Isomerization of the strands prevents breaks in the same strand that were originally broken as they separate from the junction  Branch Migration: A DNA strand in one helix is swapped with the DNA strand in the other helix. These produce regions in DNA called heteroduplexes  Resolution: recreates two separate chromosomes Gene Conversion Gene conversion: one allele is converted to the allele on the homologous chromosome  The transfer is unidirectional o This means that if one allele has a mutation that is harmful, it can be transferred by gene conversion to the second allele Gene Transcription and RNA Modification Transcription is the first step in extracting the information from a primary DNA sequence DNA sequences provide the information for transcription o Variation (mutation) always happens at the level of DNA replication Proteins must interact with the DNA sequences to regulate transcription o Recall: heterochromatin and euchromatin. Euchromatin is the open form and the only one that proteins can interact with RNA: a single strand or chain of nucleotides. Composed of a base sugar and the phosphate group.  RNA is composed of 4 bases—A, G, C and U o U replaces what would be a T in DNA  Making RNA occurs through transcription o Transcription begins within the nucleus of a cell o The first step involves separating DNA into two separate strands  This requires breaking of hydrogen bonds  Question: What is required to break hydrogen bonds?  One of the two strands is a template—this strand is used to help RNA correctly pair bases (G with C and U with A) o Stages of transcription: Initiation, Elongation, and Termination.  All of the stages will require protein to interact with the DNA o RNA Polymerases  RNA polymerase 1: used to transcribe ribosomal (rRNA) genes  RNA polymerase 2: used to transcribe all structural genes (mRNA)  RNA polymerase 3: used to transcribe transfer RNA (tRNA)  Eukaryotic Structural Genes o Eukaryotic promoter: contains a transcriptional start site—this is known as the TATA box—and a regulatory elements o Core Promotor: short and consists of a TATAAAA sequence  This sequence is known as the TATA box  TATA box usually contains about 25 base pairs o This will determine where transcription starts  Basal Transcription: when the core promotor produces a low level of transcription on its own  Regulatory elements will influence whether the RNA polymerase to recognize the core promotor o Enhancers: activating sequences o Silencers: repress transcription o Regulatory Transcription Factors: proteins that will bind to regulatory regions  Regulatory elements can be located a good distance from the gene that is in the process of being transcribed o Cis-Acting Elements: Things that have the ability to influence a nearby gene  TATA Box, enhancers, and silencers are known as cis acting elements o Trans-Acting Elements: these are produces by regulatory genes. They can be located a good distance away from the gene being transcribed RNA Modifications 5’ caps and 3’ tails  Capping: Mature mRNA’s will have a 7-methylguanosine cap at the 5’ end. o This gives certain RNA’s the ability to exit the nucleus o The cap begins and is involved early in translation o Also can be involved with splicing introns at the 5’ end  PolyA tail: added to the 3’ end and occurs by a string of adenine nucleotides being added o This requires a polyadenylation sequence o Important for the stability of mRNA  PolyA-binding proteins recognize the poly A tail to promote this stability  The length of the tail will affect how stable the mRNA ends up o Newly transcribed mRNA has a polyA tail that averages 200 nucleotides o As mRNA ages, cellular exonucleases shorten the polyA tail  Once shortened down to 10-30 nucleotides, the polyA binding proteins can no longer bind and the mRNA is degraded very quickly  Reverse transcription: can take processed mRNA molecule and turn it to a double stranded RNA/DNA hybrid that cannot be translated and can be integrated anywhere in the genome. A special reverse transcription polymerase is used to achieve this. o Processed Pseudogene: Since this sequence has already been spliced it is shorter than that of the original locus  These can have negative effects such as over production of a protein.  This is due to the pseudogenes having an open reading frame intact that is able to be transcribed and translated Splicing  Eukaryotic organisms have coding sequences (exons) and intervening sequences (introns) o Introns were first detected by comparing the base sequences of genes with the base sequences of mRNA  Transcription makes the entire gene sequence, the introns are then removed and the exons are spliced together in a process known as RNA splicing Alternative Splicing  Alternative splicing can procude several different patterns of exons in mRNA o This produces proteins with differences in amino acid sequences  May cause slight variation in protein function, which could be important during embryotic life and development.  Constitutive exons: marked this if they are not detected as being spliced out by a splicing reaction o Ex.) first or terminal exons o Always found in mature mRNA o Alternate exons are not always found in mRNA Translation  RNA Protein  Occurs in the cytoplasm  Involved interactions of mRNA, tRNA and rRNA  Know how to read the genetic code table!! (How to tell what codons produce what proteins)  Degenerate genetic code: when more the one codon specifies for the same amino acid  Cells contain many tRNA molecules (anticodon sequences) o Anticodon is a three nucleotide sequence that is complementary to each codon (following base pairing rules) o Each tRNA carries one of the 20 amino acids o Binds to the mRNA via base pairing and the tRNA “drops off” the amino acid o First codon in any living organism is “AUG”. The tRNA carries the anticodon “UAC” (methionine).  Therefore, the first amino acid of any protein is methionine  Translation continues as the ribosome moves along the mRNA one codon at a time. o Process will stop when the ribosome comes to a “stop” codon  There are 3 stop codons—refer to the genetic code table  Once this occurs translation ends and mRNA and the ribosome separate  Ribosome is the site of translation in both bacterial and eukaryotic cells o They have discrete sites (P,A,E)  Translation has three stages o Initiation  Involves the binding of mRNA, tRNA and ribosomal subunits o Elongation  Adds amino acids, one at a time to the polypeptide chain. It does this in steps  A charged tRNA binds to the A site  The enzyme peptidytransferase catalyzes bond formation between the polypeptide chain and the amino acid that is currently in the A site  The ribosome trans locates one codon to the right (3’)  The uncharged tRNA is released from the E site  Process is repeated until a stop codon is reached o Termination  Occurs once a stop codon is reached  Translation is complete  Directionality of the polypeptie chain o Has directionality that parallels the mRNA chain o The first amino acid of the polypeptide is considered to be at the N- Terminal end (or amino terminal end) o The last amino acid is considered to be at the C-Terminal end (or the carboxyl terminal end)  Protein Structure o The net result of transcription and translation is a polypeptide with a define amino acid sequence  This sequence is known as the primary structure o To become functional the polypeptides must fold and become 3D Structure and function of tRNA  Functions o Recognizes codons within mRNA and carry out the correct amino acid to the site of polypeptide synthesis o Binds to mRNA as an anticodon during mRNA-tRNA recognition  Structure o Three stem loop structure o Contains a variable region o An acceptor with a 3’ single stranded region  Aminoacyl-tRNA Synthetases o An enzyme that catalyzes the attachment of amino acids to the 3’ end of the tRNA  About 20 different forms of this enzyme per one amino acid  Once the amino acid is attached to the tRNA it is referred to as a charged tRNA  Wobble Rule o Genetic code is degenerate. o For most amino acid codons the third base is not crucial to identifying the amino acid. Transcription Factors  Transcription factors: proteins that influence the ability of the RNA polymerase to transcribe a gene o General transcription factors take the RNA polymerase and bind it to the core promotor o Regulatory transcription factors regulate the rate of gene transcription  Domains: regions of transcription factors that have specific functions  Motif: a domain that has similar structure in many different proteins  Regulatory transcription factors can be enhancers or silencers  If they up-regulate they are enhancers  If they down-regulate they are silencers  Orientation independent or bidirectional  Proteins typically recognize cis regulatory sequence elements o Noncoding DNA sequences are called response, control, or cis regulatory elements.  These are the “on/off” switches we learned about in the first module  Activators: increase the rate of transcription o Enhancer: is the DNA sequence that the activator binds to  Repressors: decrease the rate of transcription o Silencer: the DNA sequence that the repressor binds to  Homodimer: two identical transcription factors that come together  Heterodimer: two different factors that interact TATA box binding Factor (TF11D) and Mediator  Most regulatory transcription factors do not bind directly to RNA polymerases, instead they interact with either (TF11D) or the mediator o Activator proteins increase rate of transcription by interacting with the coactivators but do not bind to the DNA itself o Repressors inhibit the rate of transcription by binding to the TF11D Modulating Regulatory Transcription Factor Function  Regulatory transcription factors must be regulated for the same reasons as genes  Three basic mechanisms of regulation 1. Binding of an effector molecule (ex.) steroid hormones) a. Steroid Receptors: Regulatory transcription factors that interact with steroid hormones i. Synthesized by endocrine glands SNP’s and their Influence on gene expression  SNP’s occur during errors in DNA replication  Transcription o SNP’s in cis-regulatory sequences (enhancers, silencers, promotors) can impact the transcriptional activity of a locus  Occurs at low rates o Introns don’t have a function so SNP’s occurring here are neutral and occur at neutral rates  Splicing o SNP’s occurring in the 5’ GT or 3’ AG consensus splicing acceptor and donor sites are occurring at very low rates because they can be highly deleterious. o SNP’s can occur in exons and create cryptic GT and or AG sites o SNP’s occurring in the third position of a codon occur at a faster rate than those in the first position of a codon o SNP’s occurring in the coding region can lead to a stop codon  This would be considered a nonsense mutation o SNP’s that lead to a change in amino acid sequence (nonsynonymous) occur at a lower rate then synonymous Population Genetics  Population: group of individuals of the same species that can interbreed with one another o Genetic Polymorphism: observation that many traits display variation within a population  This is caused by two or more alleles for a trait in a population (polymorphic) o Monomorphic trait: exist in single allele in the population  Found in 99% of the population o SNP’s (single nucleotide polymorphisms): single nucleotide differences in alleles of a gene  Very common in a population Go over and understand how to do Hardy-Weinburg problems!


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