New User Special Price Expires in

Let's log you in.

Sign in with Facebook


Don't have a StudySoup account? Create one here!


Create a StudySoup account

Be part of our community, it's free to join!

Sign up with Facebook


Create your account
By creating an account you agree to StudySoup's terms and conditions and privacy policy

Already have a StudySoup account? Login here

3/4-3/7 Notes: Mutations

by: Cara Cahalan

3/4-3/7 Notes: Mutations Bios 312

Cara Cahalan
GPA 3.8

Preview These Notes for FREE

Get a free preview of these Notes, just enter your email below.

Unlock Preview
Unlock Preview

Preview these materials now for free

Why put in your email? Get access to more of this material and other relevant free materials for your school

View Preview

About this Document

On Exam 3 and Final
Karrie Weber
Class Notes
25 ?




Popular in Microbiology

Popular in Biology

This 3 page Class Notes was uploaded by Cara Cahalan on Wednesday January 13, 2016. The Class Notes belongs to Bios 312 at University of Nebraska Lincoln taught by Karrie Weber in Spring 2016. Since its upload, it has received 22 views. For similar materials see Microbiology in Biology at University of Nebraska Lincoln.


Reviews for 3/4-3/7 Notes: Mutations


Report this Material


What is Karma?


Karma is the currency of StudySoup.

You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!

Date Created: 01/13/16
3/4­ 3/7: Microbial Genomics: Mutations 10.1­10.4  Readings: 6.1­6.4, 6.10­6.13 I: Investigating Genomics  6.1 Introduction to Genomics   Genomics­ mapping, sequencing, analyzing, and comparing genomes   Bacterial genome range: 0.5­13 Mbp.  Human genome­ 3 million base pairs  6.2 Sequencing Genomes  Sequencing­ precise order of subunits in a macromolecule, order in which the nucleotides are aligned   Generations of DNA sequencing:  o First gen­ dideoxy method, Fred Sanger   Dideoxynucleotides to block chain extension, and using labeled precursors for detection   DNA primers used (more stable than RNA primers)   Copied ssDNA and dideoxynucleotides are added for each base. Analog is a chain termination  reagent (lacks 3’ –OH), inserted randomly  Shotgun sequencing­ preparation of DNA for sequencing, genome cleaved and cloned. Detect  overlapping sequences and assembled into correct order o Second gen­ massively parallel methods   Samples are sequence side by side, requires increased computing power (100x faster)   Each time dNTPs energy released for lucrifase (light­emitting enzyme)  o Third gen­ sequences single DNA molecules, needs two model features:   Allows detection of single flashes of light for single nucleotides   Fluorescent tags attached to the pyrophosphate is discarded  burst of color o Fourth gen­ post light sequencing­ measures release of protons when a new dNTP is added   Pore detector­ DNA moves through and electrical changes indicate the type of nucleotide   Genome assembly­putting fragments in correct order and eliminating overlaps   Annotation­ identifying genes and other functional regions in the genome   Closed genome­ entire genome sequence is determined, more expensive and require more human input  6.3 Bioinformatics and Annotating Genomes   Bioinformatics­ storage and analysis of structures of nucleic acid and proteins in the genome   Microbial genomes consist of ORFs separated by short regulatory regions and transcriptional terminators  Functional ORF­ encode a protein   To find an ORF, need to identify the start and stop codons in each sequence  II: Microbial Genomes  6.4 Genome Size and Content  Comparative genomics­ compares genomes based on size, organization, and gene content   Each Mbp of DNA in prokaryotes encodes about 1000 ORFs o As prokaryotic genomes increase, gene number increase proportionally (not true of Eukaryotes­ introns)  Autotrophs need fewer genes than heterotrophs   Eukaryotes have large introns, prokaryotes do not, more genes than eukaryotic genomes despite having less DNA  Genomes are modeled by adaptation to an organisms life   Comparative analysis help identify genes that code for enzymes   Genes of protein synthesis overtake metabolic genes on a percentage basis as genome size decrease  Proteins involved in:  o Core cellular processes­ minor variations in gene number and genome size  o More specialized­ more variation   Larger genomes are able to have more specialized metabolic genes due to increased competition in environment 6.10 Metagenomics   Metagenomics­ analyzes pools of RNA or DNA from environmental sample  o Metagenome­ gene content of the organisms inhabiting a certain environment (most are viruses)   Microbiome­ collection of prokaryotic cells in humans  IV: Evolution of Genomes  6.11 Gene Families, Duplications, and Deletions  Homologs­ genes that are related due to shared evolutionary ancestry   Paralogs­ related genes due to gene duplication in evolution of organism   Orthologs­ genes found in one organism that are similar to another because of a common ancestor  After duplication­ one duplicate can evolve and other supplies cell with original function  microbial evolution  6.12 Horizontal Gene Transfer and Genome Stability   Horizontal gene transfer­ transfer of genetic material from one cell to another  o 3 mechanisms: transformation, transduction, and conjugation  o Horizontally transferred gens encode metabolic functions and virulence genes 6.13 Core Genome versus Pan Genome   Core­ shared by all strains of a given species, typical of species as a whole  Pan­ core plus optional extras present in one or more strains, but not all, include mobile elements of some strains   Chromosomal islands­ extra blocks of genetic material in chromosome, contain non­crucial specialized functions o Presumed to have foreign origin because:   Flanked by inverted repeats  whole region was inserted into a chromosome   Base composition/codon bias are different than the genome proper  Found in some strains of a species and not others  o Encode virulence factors (special proteins that help initiate disease) on pathogenicity islands  Lecture:   Mutations: o Induced­ those made deliberately  o Spontaneous­ occur without human intervention, exposure to natural radiation or oxygen radicals   Base pair substitution:  o Point mutation­ change only one base pair, can lead to single amino acid change in protein or no change   Normal protein­ wild type  Silent­ does not affect amino acid sequence   Nonsense­ codon becomes stop codon, polypeptide and protein is incomplete  Missense­ amino acid changed, polypeptide altered, faulty protein formed  o Reversible through a reversion alteration in DNA that reverses effects of prior mutation  Revertant­ strain in which original phenotype that was changed in the mutant is restored   Same­site­ restored at same site as original mutation   Second­site­ mutate different site, compensating for the effect of the original mutation  o Frame shift: deletion/insertion that result in shift in reading frame, result in complete loss of gene function  Insertion +1, deletion ­1  Deletions do not revert, insertions can revert if a subsequent deletion alters reading frame  Transitions­ one purine base (A/G) is substituted for another purine; or one pyrimidine base (C/T) for another o AG GA or CT  TC  Transversions­ point mutation where purine base is substituted for a pyrimidine base, vice versa   Mutagenesis: spontaneous mutation frequencies  ­6 ­7 o 10  to 10  per kilobase pair during a single round of replication o Mutation rates in an RNA genome are higher because comparable RNA repair mechanisms don’t exist  o Perfect fidelity in organisms is counterproductive  prevents evolution  Mutagens: chemical, physical, or biological agents that increase mutation rates   o Chemical:  Nucleotide base analogs: resemble nucleotides  Chemical mutagens that induce chemical modifications or cause frameshift mutations o Physical: (electromagnetic radiation)   Nonionizing­ (UV radiation) purines and pyrimidines strongly absorb UV  Ionizing (i.e., X­rays, cosmic rays, and gamma rays)  Produce free radical that damage macromolecules in the cell  Ames Test: bacterial mutations detect for potentially hazardous chemicals  o Looks for an increase in mutation of bacteria in the presence of suspected mutagen  DNA repair systems o Direct reversal: mutated base is still recognizable and can be repaired without referring to other strand o Repair of single strand damage: damaged DNA removed and repaired using opposite strand as template o Repair of double strand damage: a break in the DNA, requires more error­prone repair mechanisms  o SOS system­ regulon, repairing dsDNA proceed without template, more error prone.    When DNA damage is large scale, the cell may use a different type of repair system  Allows replication to proceed and cell to replicate  Translesion synthesis allows DNA to be synthesized with no template  Two proteins regulate: LexA (repressor) RecA (activated in presence of DNA damage)   Selectable and non­selectable mutations:  o Selectable­ mutant has growth advantage under certain environmental conditions  Useful in genetic research, mutant capable of growing on culture containing previous mutagen  o Non­selectable mutations­have neither an advantage nor a disadvantage over the parent  Screen is more tedious than selection, methods that facilitate screening  o Replica plating­ identifies cells with growth requirement   Master plate with growth medium pressed onto velveteen which is imprinted of all colonies   Complete and minimal mediums, transfer imprint of colonies to fresh media  All colonies grow, mutants do not grow  Key Concepts:   Mutations can arise spontaneously or as a result from exposure to a mutagen  These mutations can have no effect, positive effect, or negative (cell death)  Perfect fidelity in organisms is counterproductive because it prevents evolution


Buy Material

Are you sure you want to buy this material for

25 Karma

Buy Material

BOOM! Enjoy Your Free Notes!

We've added these Notes to your profile, click here to view them now.


You're already Subscribed!

Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'

Why people love StudySoup

Bentley McCaw University of Florida

"I was shooting for a perfect 4.0 GPA this semester. Having StudySoup as a study aid was critical to helping me achieve my goal...and I nailed it!"

Jennifer McGill UCSF Med School

"Selling my MCAT study guides and notes has been a great source of side revenue while I'm in school. Some months I'm making over $500! Plus, it makes me happy knowing that I'm helping future med students with their MCAT."

Jim McGreen Ohio University

"Knowing I can count on the Elite Notetaker in my class allows me to focus on what the professor is saying instead of just scribbling notes the whole time and falling behind."

Parker Thompson 500 Startups

"It's a great way for students to improve their educational experience and it seemed like a product that everybody wants, so all the people participating are winning."

Become an Elite Notetaker and start selling your notes online!

Refund Policy


All subscriptions to StudySoup are paid in full at the time of subscribing. To change your credit card information or to cancel your subscription, go to "Edit Settings". All credit card information will be available there. If you should decide to cancel your subscription, it will continue to be valid until the next payment period, as all payments for the current period were made in advance. For special circumstances, please email


StudySoup has more than 1 million course-specific study resources to help students study smarter. If you’re having trouble finding what you’re looking for, our customer support team can help you find what you need! Feel free to contact them here:

Recurring Subscriptions: If you have canceled your recurring subscription on the day of renewal and have not downloaded any documents, you may request a refund by submitting an email to

Satisfaction Guarantee: If you’re not satisfied with your subscription, you can contact us for further help. Contact must be made within 3 business days of your subscription purchase and your refund request will be subject for review.

Please Note: Refunds can never be provided more than 30 days after the initial purchase date regardless of your activity on the site.