Shared Flashcard Set

Details

Unit 3 - Freitag
Microbial Genetics Chp7 / Recombinant DNA Technology Chp8 / Characterizing and Classifying Viruses, Viroids, and Prions Chp13
156
Microbiology
Undergraduate 2
03/21/2012

Additional Microbiology Flashcards

 


 

Cards

Term
Events in RNA Processing - Eukaryotic
+ Descriptions of Events
Definition
1. Capping - modified guanine nucletide is added to the front of the mRNA
2. Polyadenylation - addition of 100-250 adenine to end of mRNA
3. Splicing - Removal of introns and splicing together of exons.
Term
Eukaryotic difference in RNA Transcription:
Eukaryotic Bacteria
Where:
# of nuclear polymerase:
Is processing necessary:
Definition
Eukaryotic: Bacteria:
Inside Nucleus Cytosol
Three One(Sigma Factor)
Yes No
Term
Types of Transcription Termination and descriptions
Definition
Self Termination - uses a terminator sequence rich in guanine + cytosine followed by a region rich w/adenine.

Rho Dependent Termination - uses a protein molecule to signal termination.
Term
Differences:
RNA Polymerase
from
DNA Polymerase
Definition
1. in RNA poly no helicase is necessary
2. in RNA poly no primer is needed
3. in RNA only one strand is transcribed
4. RNA poly is slower than DNA Poly III ~ 50 nucleo p/sec
5. RNA uses ribose sugar DNA uses deoxyribose
6. Uracil is used instead of thymine
7. in RNA proofreading is less efficient - 1 error per 10,000 nucleotides.
Term
Where does the energy needed to covalently bond ribonucleotides come from?
Definition
Using the energy from the first phosphate bond of the ribonucleotide.
Term
Four type os RNA ribonucleotides
Definition
rATP
rUTP
rGTP
rCTP
Term
Primase Transcribes:
RNA Polymerase Transcribes:
Definition
Primase: RNA Primer
RNA Poly: mRNA, rRNA, tRNA
Term
The strength of the promoter directly affects:
Definition
The likelihood that transcription will take place.
Term
In bacteria this subunit of RNA polymerase is necessary for recognition of a promoter.
Definition
Sigma Factor
Term
RNA Polymerase initially bonds to where?
Definition
Promoter Sequences
Term
What enzyme synthesizes RNA
Definition
RNA Polymerase
Term
Start Codon:
Definition
AUG
Term
Stop Codons:
Definition
UAA
UAG
UGA
Term
# of ribonucleotides in an tRNA molecule?
Definition
75
Term
What is "Wobble" in reference to anticodon.
Definition
Change of angle from normal axis that allows the third nucleotide to hydrogen bond to a nucleotide other than its compliment.
Term
Three sites on a ribosome involved in polypeptide formation.
Definition
A - Amino Acid
P - Polypeptide
E - Exit
Term
Stages of Translation.
Definition
Initiation
Elongation
Termination
Term
Steps of Translation Initiation:
Definition
1. Ribosomal subunit attaches to mRNA at a ribosome-binding site in a way that the start codon is in the P site.
2. tRNA attaches at the ribosome's P site.
3. The larger ribosomal subunit then attaches to form a complete initiaion complex.
Term
Steps of Translation Elongation:
Definition
1. The transfer RNA whose anticodon matches the next codon delivers its amino acid to the A site.
2. A peptide bond is formed between terminal amino acid of the growing chain and the newly introduced amino acid.
3. The ribosome then shifts the mRNA one position.
4. The ribosome releases the empty tRNA from the E site.
Term
Steps of Translation Termination:
Definition
Proteins called release factors halt elongation and the ribosome dissociates into its subunits.
Term
Translation differences in Eukaryotes:
Definition
1. Initiation of translation in eukaryotes occurs when the small ribosomal subunit binds to the 5' guanine cap rather than a specific nucleotide sequence.
2. The first amino acid in eukaryotic polypeptides is methionine rather than formylmethionine.
Term
Two types of bacterial gene expression regulation:
Definition
Induction
Repression
Term
Inducible operons:
Definition
Not usually transcribed and must be activated by inducers.
Term
Repressible Operons:
Definition
Are transcribed continually until deactivated by a repressor.
Term
What are miRNA's?
Definition
Micro RNA's made of 22 nucleotides that binds with RNA silencing complex either cleaves the mRNA molecule or binds to it blocking its entrance into a Ribosome.
Term
What are siRNA's?
Definition
Double stranded RNA that binds with RNA silencing complex and blocks mRNA from binding with a ribosome. These are not natural, lab created.
Term
What is a riboswitch?
Definition
A RNA molecule that changes shape in response to environmental conditions such as temp or concentration of nutrients. When activated it will fold to either favor or block translation.
Term
Example of an inducible operon:
Definition
The lac operon - Lactose.
Term
Example of a repressible operon:
Definition
The trp operon - Tryptophan.
Term
Define biotechnology:
Definition
The use of microorganisms to make practical products.
Term
Tools of Genetic Engineering:
Definition
1. Mutagens
2. Reverse Transcriptase
3. Synthetic Nucleic Acids
4. Restriction Enzymes
5. Vectors
Term
What are mutagens?
Definition
Physical and chemical agents that produce mutations.
Term
What is reverse transcriptase?
Definition
Technique that creates a flow of genetic information in the opposite direction of conventional transcription. Therefore writing additional code to a cells DNA.
Term
What are synthetic nucleic acids?
Definition
Lab grown nucleotides.
Term
What are restriction enzymes?
Definition
Enzymes that cut DNA molecules at restriction sites (palindromes).
Term
Types of ends produced by restriction enzymes and a description.
Definition
Sticky Ends: Ends are fragmented.

CGA AGCTTCG
GCTTCGA AGC

Blunt Ends: Both strands cut at same point.

CCCAAC GTTGGG
GGGTTG CAACCC
Term
What are vectors?
Examples of Vectors:
Definition
Nucleic acid molecules used to transport and insert genes into cells.

Examples: Viral Genomes, Transposons, and Plasmids
Term
Techniques of Genetic Engineering:
Definition
1. Polymerase Chain Reaction
2. Gel Electrophoresis
3. Southern Blot
4. DNA Microarrays
5. Inserting DNA into Cells
Term
What is Polymerase Chain Reaction?
Definition
Technique by which scientists produce a large number of identical molecules of DNA in vitro.
Term
What is Gel Electrophoresis?
Definition
Technique used to isolate fragments of DNA molecules that can be inserted into Vectors.
Term
What is Southern Blot?
Definition
A method to transfer DNA from agarose gels to nitrocellulose membranes.
Term
What are DNA Microarrays?
Definition
An array consisting of molecules of single-stranded DNA, which is immobilized on glass slides, silicon chips, or nylon membranes.
Term
Three artificial techniques for introducing DNA into cells:
Definition
1. Electroporation: Usage of electrical current to puncture tiny holes in the cells membrane so DNA can enter.
2. Protoplast fusion: Combining of DNA by increasing rate of fusion.
3. Injection: By micropipette.
Term
Some products produced by recombinant DNA Technology:
Definition
Vaccines, DNA fingerprinting, Herbicides
Term
Parts of DNA:
Definition
Deoxyribose Sugar
Nitrogenous Base
Phosphate Group
Term
Eukaryotic Genomes:
Shape -
Contained Within -
Definition
Linear Shape
Contained within the nucleus
Term
What are nucleosomes?
Definition
DNA and Histones wrapped together.
Term
What are chromatin fibers?
Definition
Nucleosomes clumped together with other proteins.
Term
Other than the nucleus where else can Eukaryotic DNA be found?
Definition
Within mitochondria or chloroplasts.
Term
Define: Gene
Definition
Specific sequences of nucleotides that code for polypeptides or RNA molecules.
Term
Describe: Base Pairs
Definition
The specific way which one of 5 nitrogenous bases are hydrogen bonded to one another.
Term
Which base pair are triple bonded?
Which are double bonded?
Definition
Triple = Guanine and Cytosine
Double = Adenine and Thymine
Term
The two strands of DNA are called?
(Hint: orientation)
Definition
Antiparallel
Term
Which bacteria have histones?
Definition
Archaea
Term
Direction of DNA synthesis:
Definition
5' to 3' direction
Term
Why is DNA replication called semi-conservative?
Definition
New DNA is composed of 1 original strand and 1 daughter strand.
Term
What is a Heterochromatin?
Definition
Closed, inactive DNA
Term
What is a Euchromatin?
Definition
Open, active DNA.
Term
Genetic Recombination:
Transduction and Steps
Definition
The transfer of DNA from one cell to another via a replicating virus.

1. Phage injects its DNA
2. Phage enzymes degrade host DNA
3. Cell synthesizes new phages with phage and host DNA.
4. Transducing phage injects donor DNA into new cell.
5. Donor DNA is incorporated into recipient chromosome by recombination.
Term
Genetic Recombination:
Transformation
Definition
Recipient cell takes up DNA from the environment, such as DNA from dead organisms.

-Mouse Experiment
Term
3 Effects of Mutations
Definition
Silent Mutation
Missense Mutations
Nonsense Mutations
Term
What is a Silent Mutation
Definition
No change to amino acid sequence due to redundancy of genetic code.
Term
What is a Missense Mutation
Definition
Triplet still codes a protein but is not the correct protein in the sequence, can prevent protein from forming correctly if in a critical area.
Term
What is a Nonsense Mutation
Definition
Changes an amino acid into a stop codon.
Term
Types of Mutations
Definition
Point Mutations
Framshift Mutations
Gross Mutations
Term
What are point mutations?
Definition
One nucleotide base pair is affected.
Term
What are frameshift mutations?
Definition
When insertions or deletions cause the entire sequence to shift.
Term
What are gross mutations?
Definition
Large deletions, transpositions, or inversions of genetic sequences.
Term
Define: Mutation
Definition
A permanent change in the nucleotide base sequence of a genome.
Term
What is an Operon?
Definition
Section of DNA that includes a promoter, operator, and subsequent genes.


Operon
[----------------------------------------]
{AAAA}{=Promotor=}{=Operator=}{=Gene1=}{=Gene2=}{AAAAAAA}
Term
What are triplets?
Definition
A sequence of 3 nitrogenous bases.
Term
What are codons?
Definition
Triplets of mRNA that code for a specific anti-codon or amino acid.
Term
What are anti-codons?
Definition
Matching base pairs to codons, located on tRNA.
Term
What bases are methylated in:
Bacteria
Eukarya
Definition
Bacteria: Adenine and rarely Cytosine
Eukarya: Cytosin only.
Term
Differences in Eukaryotic and Bacteria DNA replication:
Definition
1. Eukaryotic uses four different polymerases.
2. Eukaryotic Okazaki fragments are shorter than bacterial.
3. Plants and animals methylate cytosine bases exclusively.
4. Large size of Eukaryotic chromosomes requires thousands of origins instead of one like bacterial cells.
Term
4 Types of Eukaryotic Polymerases
Definition
Alpha(1) - Initiates
Delta(4) - Elongates Leading Strand
Epsilon(5) - Replicates Lagging Strand
Gamma(3) - Replicates Mitochondrial DNA
Term
Bacteria Archaea Eukarya

# Chromo

Plasmids?

DNA Shape

DNA Locale

Histones?
Definition
|Bacteria | Archea | Eukarya
|___________|___________|_________
# Chromo| Haploid | Haploid | Diploid
|___________|___________|_________
Plasmid?| In some | In Some |Fungi\Pro
|___________|___________|_________
DNA Shp | Circular | Circular | Linear
|___________|___________|_________
DNA Loc | Nucleoid | Nucleoid | Nucleus
| Plasmids | Plasmids | Mitochon
|___________|___________|_________
Histones| No | Yes | Yes
|___________|___________|_________
Term
Topoisomerase
Definition
Removes supercoils during DNA replication of bacteria, and unwinds DNA for replication in eukaryotes.
Term
DNA Ligase
Definition
Seals gaps between Okazaki Fragments of lagging strand.
Term
RNA Primer (Primase)
Definition
Provides 3' hydroxyl group required by DNA polymerase.
Term
DNA Polymerase I
Definition
Replaces RNA primer w/DNA
Term
DNA Polymerase III
Definition
The usual enzyme of DNA replication in bacteria and mitochondria.
Term
DNA Polymerase
Definition
Adds new nucleotides into open DNA strands.
Term
DNA Helicase
Definition
Breaks hydrogen bonds.
Term
Why is one strand of DNA called the 3' strand?
Definition
Because it ends with a hydroxyl group bound to the 3' carbon.
Term
Why is one strand of DNA called the 5' strand?
Definition
Because it ends with a phosphate group attached to the 5' carbon.
Term
Roles of Methylation in Bacteria (4)
Definition
1. Control genetic expression
2. Initiation of DNA replication
3. Protection against viral infection
4. Repair DNA
Term
DNA Replication: Steps (5)
Lagging Strand
Definition
1. Primase synthesizes RNA primers, instead of 1 like leading strand it inserts one every 1000-2000 DNA base pairs.
2. Nucleotides pair up compliments.
3. DNA Polymerase 3 joins nucleotides into Okazaki fragments.
4. DNA polymerase 1 replaces RNA primers of okazaki fragments and proofreads.
5.DNA ligase seals gaps between okazaki fragments.
Term
DNA Replication: Steps (5)
Leading Strand
Definition
1. Enzyme primase synthesizes a short RNA molecule complementary to DNA strand.
2. Triphosphate deoxyribonucleotides form compliments.
3. Using energy from Triphosphate deoxyribonucleotides, DNA polymerase 3 forms covalent bonds.
4. DNA Polymerase 3 proofreads the strand.
5. DNA polymerase 1 replaces RNA primer w/DNA.
Term
Enzyme responsible for Proofreading Replicated DNA and correcting errors?
Definition
Proofreading Exonuclease
Term
DNA Replication: Initial Steps (4)
Definition
1. Proteins and histones are removed.
2. DNA Helicase separates strands.
3. DNA Polymerase binds to each strand.
4. Begin leading and lagging strand synthesis.
Term
Types of Plasmids and their Functions
Definition
Fertility - instructions for conjugation
Resistance - carry genes for resistance to drugs.
Bacteriocin - produce toxins to kill competititve bacteria.
Virulence - carry instructions for structures, enzymes, or toxins that enable it to be pathogenic.
Term
Prokaryotic Genomes:
Where is DNA stored?
Where are chromosomes located?
Definition
In Chromosomes or plasmids.
Within the nucleoid region.
Term
Define: Genome
Definition
The entire genetic compliment of a cell or virus. Including its genes and nucleotide sequences.
Term
Genetic Recombination: Conjugation (Process)
Definition
1. Bacteria connect via pili.
2. One strand of F plasmid DNA transfers to the recipient.
3. A single strand of plasmid DNA is synthesized to compliment the transfered single strand DNA.
4. The new double strand DNA is now a fully formed plasmid within the recipient cell.
Term

What is gene therapy?

 

Risks?

Benefits?

Limitations?

Definition

A process where missing or defective genes are replaced with normal copies. 

 

Risks: Unexpected Results

Benefits: Curing "uncurable" diseases.

Limitations: Limited to only certain diseases.

Term
Human genetic defects targeted by gene therapy.
Definition
Cystic Fibrosis
Sickle-cell anemia
Hemophilia
Diabetes
Term
What is DNA Fingerprinting
Definition
Technique to identify unique sequences of DNA.
Term
What are some applications for DNA Fingerprinting?
Definition
Paternity Investigations
Crime Scene Forensics
Diagnostic Microbiology
Epidemiology
Term
What is "Antisense" DNA Technology?
Definition
The technique of using nucleic acid molecules that have nucleotide sequences that bind to and interfere with genes and mRNA molecules.
Term
What is a GMO?
Definition
Genetically modified organism, used to produce proteins and enzymes not typically found within said organism.
Term
Novel properties of Viruses:
Definition

 

 

 

 

 

Inert outside of a cell, becomes active inside.

Do not divide or grow.

Acellular

Obligate intracellular parasites.

Contain either DNA or RNA, never both.

Genome can be dsDNA, ssDNA, dsRNA, ssRNA.

Ultramicroscopic.

Have a proteinaceous capsid around genome.

Replicate in an assembly-line manner using host cell functionality.

Term
General size of a virus is measured in?
Definition
Nanometers
Term
When a virus is outside of a cell it is referred to as a?
Definition
Virion
Term

All virions have these basic parts:

 

 

Some also have:

Definition

All: Capsid and a Nucleic Acid Core

 

Some: Envelope (Phospholipid membrane)

 

Term
The term referring to a capsid and its nucleic acid core is:
Definition
Nucleocapsid
Term
The outermost layer of a virus, either the capsid or envolope provides these funcitons:
Definition
Protection and recognition sites for specific hosts.
Term
Define: Capsid
Definition
Protein coating surrounding nucleid acid core of a virus.
Term
Define: Capsomere
Definition
The proteinaceous subunits of a capsid.
Term
A virus that infects bacteria is called?
Definition
Bacteriophage
Term
Name given to viruses that will infect many types of cells in many different hosts.
Definition
Generalists
Term
Virus is latin for:
Definition
Poison
Term
Smallest Virus size:

Largest Virus size:
Definition
Smallest: 10nm

Largest: 400nm
Term
Define: Matrix Protein
Definition
Proteins that fill the region between capsid and envelope.
Term
Define: Viral Envelope
Definition
A membrane located externally to the viral capsid.
Term
How does a capsid acquire a viral envelope?
Definition
When a virus is released from a host cell it is coated with a portion of the host cells external membrane.
Term
In addition to the viral envelope what else does the virus pick up while being exocytosed? What are these used for?
Definition
Glycoproteins, used for recognition of like cells.
Term
Chemical Composition of Capsomer:
Definition
Protein
Term
Chemical Composition of Capsid:
Definition
Protein
Term
Chemical Composition of Viral Genome:
Definition
Nucleic Acid
Term
Chemical Composition of Viral Envelope:
Definition
Phospholipid Bilayer and Proteins
Term
Chemical Composition of Viral Spike:
Definition
Glycoprotein
Term
Five stages of viral replication:
Definition
1. Attachment
2. Entry
3. Synthesis
4. Assembly
5. Release
Term
Viral Replication: Explain Attachment
Definition
Connecting of the virion to a host cell.
Term
Viral Replication: Explain Entry
Definition
A virion or its genome entering a host cell.
Term
Viral Replication: Explain Synthesis
Definition
Creation of new nucleic acids and viral proteins by the host cell's enzymes and ribosomes.
Term
Viral Replication: Explain Assembly
Definition
Building of new virions within the host cell.
Term
Viral Replication: Explain Release
Definition
Virions leaving the host cell either by lysing or exocytosis.
Term
How does lysogenic replication differ from lytic replication?
Definition
During lysogenic replication the viral DNA/RNA remains inert until and environmental trigger activates it. While inert it is inserted into the DNA of the host and is replicated with each cell division.
Term
An inactive bacteriophage is called:
Definition
Prophage
Term
3 Ways animal viruses can penetrate a host cell?
Definition
1. Direct Penetration
2. Membrane Fusion
3. Endocytosis
Term
Additional step that animal viruses must do after entering host cell:
Definition
Uncoating the Capsid.
Term
For the genome: dsDNA
How is mRNA synthesized?
What molecule is template for Genome Replication?
Definition
mRNA Synth: RNA Polymerase (in nucleus or cytoplasm)
Molecule: Each strand of DNA serves as template for its compliment.
Term
For the genome: ssDNA
How is mRNA synthesized?
What molecule is template for Genome Replication?
Definition
mRNA Synth: RNA polymerase (in nucleus)
Molecule: Complementary strand of DNA is synthesized.
Term
For the genome: +ssRNA
How is mRNA synthesized?
What molecule is template for Genome Replication?
Definition
mRNA Synth: Genome acts as mRNA
Molecule: -RNA complementary to the genome is synthesized to act as template.
Term
For the genome: +ssRNA (Retroviridae)
How is mRNA synthesized?
What molecule is template for Genome Replication?
Definition
mRNA Synth: DNA from RNA using reverse transcriptase. mRNA is transcribed from DNA by RNA polymerase.
Molecule: DNA
Term
For the genome: -ssRNA
How is mRNA synthesized?
What molecule is template for Genome Replication?
Definition
mRNA Synth: RNA dependent RNA transcriptase
Molecule: +mRNA (compliment to viral genome)
Term
For the genome: dsRNA
How is mRNA synthesized?
What molecule is template for Genome Replication?
Definition
mRNA Synth: Positive strand of genome acts as mRNA.
Molecule: Each strand acts as template.
Term
Steps of Animal Virus Replication: (6)
Definition
1. Attachment
2. Penetration
3. Uncoating
4. Synthesis
5. Assembly
6. Release
Term
What term describes a nonenveloped virus?
Definition
Naked
Term
Name given to viruses that shed from host cell slowly and relatively steadily without killing the host cell.
Definition
Persistent infections.
Term
Two ways naked viruses are released from host cells:
Definition
Exocytosis or by cell lysis.
Term
Examples of latent viruses:
Definition
Herpes and Chicken Pox
Term
Define: Lysogenic Conversion
Definition
Conversion of a harmless form of bacteria to a pathogenic form.
Term
Difference in Latency vs. Lysogeny
Definition
In latency the viral DNA does not necessarily become incorporated into the host DNA.
Term
Uncontrolled cell division in a multicellular animal is called:
Definition
Neoplasia
Term
Define: Oncogenes
Definition
Active genes that control cell division rate.
Term
Factors that contribute to the inhibition of oncogene repressors and the activation of oncogenes:
Definition
UV Light
Radiation
Carcinogens
Viruses
Term
How are viruses classified?
Definition
DNA or RNA strand type.
Term
Define: Viroids
Definition
Extremely small, circular pieces of RNA that are infectious and pathogenic to plants.
Term
Define: Prions
Definition
Proteinaceous infective particles.
Term
How do Prions infect cells?
Definition
By hijacking the cellular membrane protein PrP of the host and converting it to prion PrP.
Term
Examples of diseases associated with Prions:
Definition
Mad Cow Disease (Bovine Spongiform Encephalitis)
Scrapie in sheep.
Kuru
Chronic Wasting Disease in deer and elk.
Creutzfeldt-Jakob disease in humans.
Term
A virus that is specific for a bacterial host is called a:
Definition
Phage
Term
Name 3 criteria for specific family classification of viruses:
Definition
1. Type of nucleic acid.
2. Envelope Structure
3. Capsid Type
Term
A clear zone of phage infection in a bacterial lawn is:
Definition
A Plaque
Supporting users have an ad free experience!