Mmg 301 - Exam 3

Front 1

virus definition

Back 1

-DNA or RNA genetic element surrounded by protein coat

-able to replicate in cells as a parasite and exist in a free state

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bacteriophage definition

Back 2

a prokaryotic virus

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4 virus characteristics

Back 3

1. obligate parasites
2. protein coat around genome
3. extracellular (virion) /intracellular
4. RNA/DNA in circular/linear form

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capsid definition

Back 4

viral protein coat surrounding nucleic acid (forms nucleocapsid)

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icosahedron virus example

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phage phiX174

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filamentous virus example

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tobacco mosaic virus

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complex virus definition

Back 7

composed of multiple polymers (capsomers), found in bacteriophage (e.g. T4)

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enveloped virus definition

Back 8

mostly in eukaryotes (e.g. HIV/influenza)

host-derived membrane around icosahedral nucleocapsid

few virus-encoded proteins exposed

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contents of influenza envelope

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hemagglutinin and neuramidase

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X174 definition

Back 10

-first genome sequenced
-has overlapping genes

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overlapping gene definition

Back 11

different genes encoded in different reading frames; allow phage genome to fit into small virion

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RNA viruses

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use RNA-dependent RNA polymerase to replicate instead of DNA

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lysogeny definition

Back 13

phage integrates into host (lysogen) genome and replicates

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viruses causing cancer

Back 14

hepatitis B/C - liver cancer

papilloma virus - cervical cancer

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viruses causing lysis

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poliovirus and ebola virus

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viruses causing persistent/latent infection

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herpes simplex
varicella-zoster (VZV)
HIV
cytomegalovirus (CMV)

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retrovirus definition

Back 17

positive strand RNA viruses with a dsDNA intermediate; use reverse transcriptase enzyme to copy RNA into DNA (latent state)

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major repeats in retrovirus genomes

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terminal repeats (R) - for replication

gag - nucleocapsid proteins

pol - protease, reverse transcriptase, and integrase

env - envelope glycoproteins

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retroviral polyprotein strategy

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protease inhibitors prevent protease from cutting polyprotein into individual proteins (translation)

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genetic material directly translated into protein

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single stranded (+) RNA

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genetics

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the study of genes, the units of heredity

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mutation

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heritable change in base sequence of genome; spontaneous or induced

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selection

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only mutant will grow; powerful because large numbers of mutants can be analyzed

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screening

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no growth advantage for mutation and each mutant examined for desired phenotype

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auxotroph

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mutant strain requiring nutritional supplement for growth not needed by wild type

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prototroph

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strain not requiring additional nutritional supplement

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wild type

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form isolated from nature that has not been genetically modified or mutated

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replica plating

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type of screening commonly used to isolate auxotrophs

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open reading frame (ORF)

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part of gene that encodes a protein

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operon

Back 30

different genes co-transcribed on single mRNA (30%)

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plasmid

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self-replicating accessory coding DNA not essential for cell viability (antibiotic resistance)

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4 mutation types

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point (1bp)
insertion
deletion
inversion

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missense mutation

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point mutation changes amino acid
(most common)

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nonsense mutation

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point mutation results in stop codon

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silent mutation

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point mutation results in different codon for same amino acid

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mutation rate

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10^6-10^7 per 1000bp during 1 round of replication

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mutagenesis

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employment of chemical, physical and biological agents to generate mutations

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same site reversion

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point mutation for wild type genome

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second site reversion

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corrects defect of first mutation (e.g. restores reading frame of a frame shift mutation)

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suppressor

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mutant that suppresses a mutant phenotype

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nonsense suppressor

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tRNA anticodon mutated to read a stop codon

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auxotrophic phenotype

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-used to determine mutagenicity of substance using Ames assay

-commonly isolated using replica plating technique

-evident only on some types of media

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transposons

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DNA that hops into DNA and can
cause a null mutant (mutant totally defective)

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transformation

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uptake of free plasmid DNA into cell

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transduction

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phage mediated DNA transfer:
generalized = random
specialized = adjacent to integrated phage DNA

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conjugation

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direct cell-to-cell DNA transfer requiring cell-to-cell contact

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recombination

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exchange of genes between two genetic elements within cell; required for gene inheritance

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homologous recombination

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exchange of DNA segments from one DNA molecule to another

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competence

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DNA can be double-stranded, or degraded to single-stranded as it enters cell

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plaque

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zone of lysis on bacterial lawn

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horizontal/lateral gene transfer

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exchange of genes between two lineages of organisms

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F+ plasmid

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codes for conjugation (in E. coli)

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F+ transfer

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donates DNA as separate plasmid (F- to F+)

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Hfr transfer

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high-frequency strains in genome

DNA as F DNA and chromosome segment

used to map genetic markers

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merodiploid

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two copies of one or a few genes (e.g. wild-type and mutant gene)

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complementation

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used to determine:

-if 2 mutations are in same gene

-if wild type gene can restore function of mutant gene

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tests for mutant gene of unknown function

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1. redundancy = combine mutant gene of unknown fxn w/ every other gene of unknown fxn and look for phenotype

2. haven’t looked correctly = test mutant gene of unknown fxn in 100s of environments

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untranslated region

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DNA transcribed to mRNA but not translated (i.e. before a START and after a STOP codon)

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promoter

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site of RNA polymerase binding

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Shine-Dalgarno sequence

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ribosome-binding site

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effector

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small molecules that act as inducers (lactose) and co-repressors (tryptophan) of transcription

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feedback inhibition

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end product of biosynthetic pathway represses biosynthetic
pathway (i.e. AA biosynthesis)

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positive regulation (control)

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activation of transcription from promoters by activator proteins that bind to DNA at cis-acting activation sites

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negative regulation (control)

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inactivation of transcription from promoters by activator proteins that bind to DNA at cis-acting activation sites

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attenuation

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modulation of rate of transcription by rate of translation of leader sequence of mRNA

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riboswitching

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control of transcription by folding of a nascent RNA

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2 mechanisms for regulation of gene products

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1. control activities (feedback inhibition)

2. control amounts (transcription/translation)

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constitutively expressed genes

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not regulated

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helix-turn helix proteins

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mostly prokaryotes

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Zinc-finger proteins

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mostly eukaryotes

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inducible genes

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transcribed only when induced, and then only if promoter is activated, meaning it can be
accessed by appropriate σ factor and core RNAP

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operon

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functioning unit of genomic DNA containing gene cluster under control of single promoter

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lac operon (E. coli)

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lacZ, lacY, and lacA genes

promoter, terminator, and operator

regulator = glucose/lactose

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lacO+

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lac operator

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lacZ+

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β-galactosidase gene

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lacY+

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permease

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lacA+

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trans-acetylase

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allolactose effector

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“natural” inducer of lac operon

inactivates LacI

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isopropyl-β-D-thiogalactoside (IPTG)

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gratuitous inducer used in lab to induce lactose promoters

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E. coli on minimal medium with lactose and X-gal

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blue colonies

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E. coli on minimal medium with glucose, lactose and X-gal

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blue colonies

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group transport system

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5 enzymes for E.coli glucose uptake
sequentially transfer phosphate from phosphoenolpyruvate (PEP) to the transporter (EnzIIc), which transports and phosphorylates glucose

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β-galactosidase

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expressed in presence of lactose when glucose is low

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transcription factors before promoter

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enhance binding and promote transcription

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repressors on/after promoter

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block transcription

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catabolite activator protein (CAP) or cAMP receptor protein (CRP)

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activator; binds in the presence of cAMP effector

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LacI

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repressor; binds in absence of lactose effector

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catabolite repression in E.coli

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genes not expressed when glucose available (preferred C source)

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cyclic AMP

Back 89

a regulatory nucleotide synthesized by adenylate cyclase

effector for CRP - activates lac

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bistability

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two stable states of cells, induced and un-induced

TMG = another LacI effector

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sigma factors

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recognize specific promoters, recruit RNA polymerase, and activate transcription

expression of different sigma factors changes which genes are expressed (i.e. global regulation)

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signal transduction system

Back 92

sensor kinase: senses signal and becomes phosphorylated transducing signal by acting as kinase, transferring phosphate to

response regulator: regulatory output, binds DNA in phosphorylated form and inhibits transcription

phosphatase: removes phosphate to reset response regulator