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UH / Biology / BIOL 3301 / What is genetic redundancy?

What is genetic redundancy?

What is genetic redundancy?


School: University of Houston
Department: Biology
Course: Genetics
Professor: Chin-yo cooper
Term: Fall 2016
Tags: Genetics
Cost: 50
Name: BIOL 3301 Exam 4 Study Guide
Description: Exam 4: Chapter 16- Forward Genetics Chapter 17- Reverse Genetics Chapter 18- Genomics Chapter 19- Cytoplasmic Inheritance
Uploaded: 11/29/2016
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✰Genetics Exam 4 Study Guide✰  

What is genetic redundancy?


Chapter 16- Forward Genetics  

Chapter 17- Reverse Genetics  

Chapter 18- Genomics  

Chapter 19- Cytoplasmic Inheritance  





Forward Genetics

Define phenotype​ → ​Create mutant genes →​ identify associated genotype

What is site-directed mutagensis?

Find certain mutants→ make clones→ what do the mutants affect? → where do they reside?


Mutagenesis: Organism treated with mutagen→ genome mutations

Saturation Mutagenesis- multiple mutant alleles

Dominant Mutations- Rare , usually hypermorphic

What is structural genetics?

Mutant males bred with Wild Type females→ 50% mutant offspring

Recessive Mutations- fairly common, often null or hypomorphic

  Chemical:​ Allele Spectrum- Null, Hypomorphic, Hypermorphic, High mutation rate/locus Don't forget about the age old question of danielle alessi

Radiation:​ Allele Spectrum- Hypomorphic-often null, Hypermorphic Moderate mutation rate/locus Insertional:​ Allele Spectrum- Hypomorphic- often Null Low Mutation rate/locus If you want to learn more check out poli 203 concordia

Conditional Alleles:

Permissive condition: gene product is either functional or not needed under environmental condition Restrictive condition: gene product absent, inactive or required

Lethal conditions can be compensated for if addition of needed substance added to media, certain temp or pH etc.

Complementation Test

→ If progeny produced by two mutant alleles are wild type, mutant alleles complement- affect two different genes → If progeny of two mutant alleles are mutant, the mutations affect the same gene​, fail to complement

Interacting Genes

Modifier Screen: used to see if mutations in a second gene can modify the phenotype of the first mutation Enhancer screen- identifies second-site mutant alleles that enhance a mutant phenotype Suppressor screen- second-site mutations that suppress the first are isolated If you want to learn more check out anth 201 u of c

Synthetic Lethality-Modifier screens may identify double mutants with a phenotype more Don't forget about the age old question of eku political science

severe than of two individual mutant phenotypes→ combination of two viable mutations can

result in inviability

Genetic Redundancy​ ​Two genes encode very similar proteins, function nearly interchangeably Cannot fully compensate for each other→ mild phenotype

Due to genetic redundancy- forward genetics misses genes when reverse genetics does not. 

Recombinant DNA Technology:  

Set of techniques for amplifying​, ​maintaining​ and manipulating​ DNA (in vitro and in vivo)

  We also discuss several other topics like neutralphils







Restriction-Modification System  

Restriction Enzymes: Cleave DNA, recognize specific sequences- 4-8 base pairs; think CRISPR Blunt Ends- cut leaves no single stranded overhang → harder to recombine

Sticky Ends- can base pair with complementary sequence

Blunt ends can be converted to sticky by ligation of short oligonucleotides

Bacterial DNA sequences are methylated to protect it from restriction enzyme cleavage, recognition sequences   Don't forget about the age old question of bnad 276 university of arizona

Molecular Cloning

1. Cloning vector and donor DNA fragment

are combined to produce a ​recombinant 


2. Organisms containing copies of the

cloned DNA segment are selected

3. Recombinant clone is ​amplified​ in a

biological system

Multiple cloning sites (MCS): several

different restriction enzyme sites found in

both plasmids

Vector- carrier fragment of DNA, → Introduced into biological system where DNA is amplified

Nonrecombinant Vector- no DNA is inserted, not exhibiting the results of genetic recombination

Transgenic organism: genome which includes introduced gene(s) from other organisms

Transgene: introduced gene that integrates into genome, Includes regulatory sequences for expression cos sites: cohesive end sequences interact with lambda phage coat proteins to package the single genome units

Vector Types E. ​coli: normal host Plasmid:​ <15 kb circular DNA→ subcloning and cDNA libraries

Lambda: ​<23 kb kb Linear phage chromosome→ cDNA & genomic libraries

Cosmid:​ ~30-45 kb circular DNA → Genomic Libraries

BAC:​ ~100-200 kb Artificial Bacterial chromosome→ genomic libraries

YAC:​ ~250-2000 kb Artificial Yeast chromosome, S. cerevisiae as host

Plasmids Vectors​: prokaryotic circular chromosome: 100-200 per cell,

-Used to amplify DNA molecules, replicate independently, selectable marker: antibiotics resistance,

 Bacteriophage Vectors:​ Bacteriophage Lambda:lysogenic gene removed- 23kb of DNA can be inserted→ lytic cycle Natural system cleaves sequences into single genome units



Codon Bias​- ​Different organisms vary in the degree to which certain codons are used

Complicates transgenic insertion e.g. when different codons code for same AA

Insulin from E. ​

Precursor/Start: Preproinsulin→

1.​ Remove the 24 N-terminal amino acid → forms proinsulin 

2. ​35 additional aa are removed→ generates two amino acid chains, A and B

3.​ A and B chains joined by disulfide bonds to produce insulin




Site-Directed Mutagenesis​- Process where nucleotide changes can be made in a DNA sequence → PCR reaction with primers and essential nutrients included (PCR amplification)

→ mixture of plasmid molecules is produced (some are desired mutant)

Non-Mutant Plasmids: selectively degraded by digestion with DpnI by marking/methylating A in GATC site  → Mutant Plasmids are not methylated and therefore saved from degradation 

Integration into Host Chromosome:  

Circular DNA​: ​Single crossover- does not replace target gene Double crossover- replacement of target gene Linear DNA​: ​Single crossovers- chromosomes lost Double crossovers- replacement of target gene

Homologous recombination- Targeted; requires homology between the DNA and the site of insertion Illegitimate recombination: Untargeted; integrates introduced DNA into random locations of the genome

Chapter 17 Reverse Genetics  

Positive Selective Marker- selectable markers that confer selective advantage to the host organism. Transfection vector contains two regions of DNA homologous to the target locus next to a positive selectable marker E.g. Neomycin (Neo) gene, product of which metabolizes G418 drug, normally lethal to mammalian cells

Negative Selective Marker - counter-selectable markers that eliminates or inhibits growth of the host organism, selects against non-homologous recombination which can be lethal E.g. thymidine kinase, tk, gene from a herpes simplex virus

Integration of transgene as multicopy concatemers causes gene expression to:

→ increase due to multiple copies

→ decrease due to RNA-mediated silencing effects of repetitive sequences

→ expression can vary due to chromosomal environment at gene’s location

Transgenic Cells→ Animals  

1. ES cells are isolated and cultured (pure)

2. DNA introduced and cells transferred to medium which selects for positive marker (against negative marker) 3. Transfected cells put back in blastocyst embryo of a different mouse

4. Blastocyst inserted in phenotypically different surrogate female→ develops into chimeric mouse

Reporter Genes​- investigate gene regulation, regulatory

sequences, and monitor gene expression patterns

Transcriptional fusion​- regulatory sequences fused to reporter

gene → expressed by the regulatory sequences

Translational fusion-​ regulatory and coding sequences fused to

reporter gene → protein produced can be visualized

Pluripotent- capable of giving rise to several different cell

types. iPS cells- induced pluripotent stem cells directly from adult cells Fibroblast- a cell in connective tissue that produces collagen and other fibers Somatic Gene Therapy: designed to correct genetic defects in somatic cells, genetic alterations induced are passed onto daughter cells via mitosis, progeny will not inherit. Totipotent: capable of giving rise to any cell type or (of a blastomere) a complete embryo. 

Concatemers: DNA strand that has multiple copies of the same DNA sequence linked in series

Chimera: single organism composed of cells from different genome

Blastocyst: structure of 200-300 cells, forms after 5 days

Reverse Genetics:​ ​Genotype​ sequenced → Create mutant genes → Identify phenotypes Two Approaches:

1. Generate large collection of random insertion mutations 

and then screen for mutations using PCR.

2. Harness gene silences phenomenon called RNA 

interference (RNAi) to reduce expression of the gene of



Insertion Mutations  

Uses knockout libraries​- collection of mutants in organism, where

most or all of the genes have been annotated

RNA Interference in Gene Activity (RNAi) 

Primary role is to silence repetitive DNA: stable loss-of-function or

transient alleles Double 

Stranded RNA (dsRNA)- can act as a trigger for degradation for any

dsRNA or single-stranded mRNA complementary to it, and can also

protect against viruses  



TILLING:​ Targeted Induced Local Lesions in Genomes

Chemical mutagenesis then mutational screening (PCR)

-small and large scale, automation, high throughput

-high probability of discovering even deletion mutations

Randomly mutagenized to saturation→ PCR, denatured, reannealed, identify

mutations in the desired gene (homoduplex). Heteroduplex DNA also


Heteroduplex DNA can be distinguished by differential migration on a

gel or by different susceptibility to endonuclease digestion, not


CRISPR/CAS:​ Clustered Regularly Interspaced Short Palindromic

Repeats Prokaryotic acquired “immune” system against foreign plasmid and phage → Foreign DNA saved in spacers, stored as memory for future immune response.

Programmable ​transcription factors​ to activate target genes or silence specific genes.

Cas​ proteins use the CRISPR spacers to recognize and cut these exogenous genetic elements (like RNAi). guideRNA (gRNA)​- Designer sequences for targeting specific DNA sequences.

Chapter 18​ ​Genomics​- global/whole genome perspective of genetics

Essential components of Genomics:

High-throughput: Robotics and automation,

Comprehensive: Everything accounted for, made efficient by informatics

Highly Parallel: Parallel testing, millions of computational tests all at the same time

Structural Genetics- ​sequencing of genomes and cataloging them  

Analysis: Clone-by-clone

sequencing​- Overlapping fragments arranged in linear order to make

genome physical map

Whole-genome shotgun (WGS) sequencing-​ ​sequencing in chunks

resulting sequence assembled into contigs based on sequence


Genome annotation: identifying location of genes and functional sequences

within the genome sequence

Variation in Repetitive DNA- Interferes with genome assembly; consists of

dispersed repetitive DNA and Transposable elements

Evolutionary Genetics​- ​comparative study of genomes

Highly conserved protein-coding DNA sequences​: analyzed to identify nodes, ancient evolutionary branch points; noncoding sequence may clarify very recent nodes

Genes encoding​ rRNAs​ provide a universal sequence for comparison due to their ubiquity and high degree of conservation

Contigs- assembled overlapping genomic clones

Dispersed Repetitive DNA- repetitive DNA not located at telomeres or at centromeres

Paralogs- genes that originated by a duplication event; biologically distinct but biochemically related functions

Orthologs- genes in different species that are derived from a single ancestral gene in the species’ last common ancestor Synteny- conserved order of consecutive genes along the length of the chromosome or chromosomal segment Microsynteny- synteny at the level of only a few genes

Functional Genetics​- ​study of gene function from a whole-genome perspective

Transcription analysis: 

DNA Microarrays​-​Consist of collections of DNA fragments that act as probes which detect transcript complementary sequences, ​tests the amount of expression, where and when the gene is expressed. Cy3 is a GFP tagged to cDNA strand. Green: underexpression, Red: over expression (See on last page of review)

Expression array -carries unique sequence per annotated gene in genome

High Throughput Sequencing:​ ​RNA converted into cDNA

Sequence is compared to the reference genome sequenced to identify sequences present in the cDNA population  

Proteomics:​ the study of proteomes and their functions 


Analysis: Two-hybrid system

“Bait” and “Prey” proteins tested for interaction (puzzle pieces)

-Fused to Gal transcription factors

Œ ​Bait and prey fit together → transcription

X ​Bait and prey don’t match up→no transcription

E.g. Gal4 dimer (Gal4-AD and Gal4-BD) used to test for bait and prey

interaction (must be like puzzle pieces), see molecular cloning figure,

lacz beta-galactosidase model

Two Hybrid System cannot detect certain protein interactions:

→ interacting proteins are not efficiently transported into nucleus

→ third party interaction

Genetic Regulatory Networks-​ ​map molecular interactions, with

related function which govern gene expression levels of mRNAs and

proteins → Two genes act in the same or redundant pathways→

Identification of gene interactions can provide clues to gene function →

If gene of unknown function is found in a particular network→​ suggests a possible function for the gene Transcriptomics- study of gene expression from genomic perspective

Systems Biology- prediction of biological function based on interactions in genetic networks and other information about genes

Chapter 19 Cytoplasmic Inheritance:​ ​transmission extranuclear chromosomal genes Extranuclear Genome: Mitochondrial and chloroplast genome- ​independent of nuclear genome


Cytoplasmic Inheritance​- transmission of genes on mitochondrial and chloroplast chromosomes, Chloroplasts organelles where photosynthetic reactions convert light energy and CO2 into fixed organic carbon Mitochondria- powerhouse of cell, inner membrane location of electron transport system  

Mitochondria: th​ e Powerhouse

 Most proteins needed for mtDNA replication, transcription, and translation are encoded by nuclear genes→ product transported to mitochondria

-Circular genomes (mostly)

mtDNA is ​not​ packaged in chromatin, ​genome anchored to inner mitochondrial membrane

Mitochondrial Transcription and Translation

-mtDNA transcribed by RNA polymerase (like bacteria), encoded by mitochondrial gene and nuclear in others -Mitochondrial transcriptional regulation varies among species, reminiscent of bacterial operons -Ribosomes!

-Mitochondrial genes encode rRNAs but ribosomal proteins may be encoded for in nuclear or mitochondrial genes. Shine-Dalgarno sequences found upstream of protein-coding genes (bacterial)→ not usually the case

Cytoplasmic Inheritance differs from Nuclear Inheritance  

1. Eukaryotic cells may contain multiple organelles

2. Chloroplasts and mitochondria may contain multiple chromosome copies

3. Sizes, numbers, and identity of genes in organelles differ among species

4. Trait controlled by cytoplasmic inheritance can also be influenced by nuclear genes, joint action

Mitochondria and Chloroplasts are uniparental and of maternal origin  

-In some species, cytoplasmic organelles are contributed bi-parentally.

Mitochondria undergo frequent fusion and fission​ → potential of mixed origin genomes

→ allows for genome to become homogenized

*Chloroplasts​ usually do not undergo fusion 


Organelle Transmission Genetics​ depends on:  

1. Growth, division, and segregation of the organelles themselves

2. Nucleoid division and segregation in the organelle

3. Individual organelle genome replication

Replicative Selection- heteroplasmic cells may give rise to homoplasmic daughter cells, product of random distribution of organelles to daughter cells and the disassociation of organelle replication from the cell cycle. Homoplasmic- all copies of cytoplasmic gene are the same

Heteroplasmic- variation exists among copies of cytoplasmic genes (location)

Nucleoid: area where protein-DNA complexes are made from packaged organelle DNA

Cytoplasmic Modes of Inheritance  

1. Maternal inheritance of organelles in mammals and flowering plants

2. Paternal inheritance of alleles in gymnosperms

3. Silencing of organelles, or selective degradation, from one parent; ex.Chlamydomonas (single celled algae) 4. Biparental inheritance; ex. Saccharomyces (yeast)

Maternal Inheritance of Mitochondrial Genome in Mammals  

1. Predictions of inheritance of mitochondrial mutations based on maternal genotype only 2. Allows for specific examination of maternal lineage, helps determine migration and evolution 3. Phylogenetic trees constructed from mitochondrial DNA sequences only consider the maternal history of the species, no paternal contribution→ no allele recombination

Mitochondrial Eve:​ human migration and evolution

Multiregional (MRE) model​: 2 million years ago modern humans emerged gradually and simultaneously from Homo erectus on different continents. Predicts uniform genetic diversity.

Recent African origin (RAO) model​: 120,000-200,000 years ago modern humans evolved from a small African population that migrated out of Africa, displacing other species. More genetic diversity should be observed in the oldest populations in Africa.

mtDNA analysis supports RAO model

African populations are most diverse and diversity elsewhere is based on a subset of African alleles. Estimate minimum divergence time of humans: ~ 200,000 years


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