question

Events in RNA Processing - Eukaryotic
+ Descriptions of Events

answer

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.

question

Eukaryotic difference in RNA Transcription:
Eukaryotic Bacteria
Where:
# of nuclear polymerase:
Is processing necessary:

answer

Eukaryotic: Bacteria:
Inside Nucleus Cytosol
Three One(Sigma Factor)
Yes No

question

Types of Transcription Termination and descriptions

answer

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.

question

Differences:
RNA Polymerase
from
DNA Polymerase

answer

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.

question

Where does the energy needed to covalently bond ribonucleotides come from?

answer

Using the energy from the first phosphate bond of the ribonucleotide.

question

Four type os RNA ribonucleotides

answer

rATP
rUTP
rGTP
rCTP

question

Primase Transcribes:
RNA Polymerase Transcribes:

answer

Primase: RNA Primer
RNA Poly: mRNA, rRNA, tRNA

question

The strength of the promoter directly affects:

answer

The likelihood that transcription will take place.

question

In bacteria this subunit of RNA polymerase is necessary for recognition of a promoter.

answer

Sigma Factor

question

RNA Polymerase initially bonds to where?

answer

Promoter Sequences

question

What enzyme synthesizes RNA

answer

RNA Polymerase

question

Start Codon:

answer

AUG

question

Stop Codons:

answer

UAA
UAG
UGA

question

# of ribonucleotides in an tRNA molecule?

answer

75

question

What is "Wobble" in reference to anticodon.

answer

Change of angle from normal axis that allows the third nucleotide to hydrogen bond to a nucleotide other than its compliment.

question

Three sites on a ribosome involved in polypeptide formation.

answer

A - Amino Acid
P - Polypeptide
E - Exit

question

Stages of Translation.

answer

Initiation
Elongation
Termination

question

Steps of Translation Initiation:

answer

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.

question

Steps of Translation Elongation:

answer

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.

question

Steps of Translation Termination:

answer

Proteins called release factors halt elongation and the ribosome dissociates into its subunits.

question

Translation differences in Eukaryotes:

answer

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.

question

Two types of bacterial gene expression regulation:

answer

Induction
Repression

question

Inducible operons:

answer

Not usually transcribed and must be activated by inducers.

question

Repressible Operons:

answer

Are transcribed continually until deactivated by a repressor.

question

What are miRNA's?

answer

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.

question

What are siRNA's?

answer

Double stranded RNA that binds with RNA silencing complex and blocks mRNA from binding with a ribosome. These are not natural, lab created.

question

What is a riboswitch?

answer

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.

question

Example of an inducible operon:

answer

The lac operon - Lactose.

question

Example of a repressible operon:

answer

The trp operon - Tryptophan.

question

Define biotechnology:

answer

The use of microorganisms to make practical products.

question

Tools of Genetic Engineering:

answer

1. Mutagens
2. Reverse Transcriptase
3. Synthetic Nucleic Acids
4. Restriction Enzymes
5. Vectors

question

What are mutagens?

answer

Physical and chemical agents that produce mutations.

question

What is reverse transcriptase?

answer

Technique that creates a flow of genetic information in the opposite direction of conventional transcription. Therefore writing additional code to a cells DNA.

question

What are synthetic nucleic acids?

answer

Lab grown nucleotides.

question

What are restriction enzymes?

answer

Enzymes that cut DNA molecules at restriction sites (palindromes).

question

Types of ends produced by restriction enzymes and a description.

answer

Sticky Ends: Ends are fragmented.

CGA AGCTTCG
GCTTCGA AGC

Blunt Ends: Both strands cut at same point.

CCCAAC GTTGGG
GGGTTG CAACCC

question

What are vectorsExamples of Vectors:

answer

Nucleic acid molecules used to transport and insert genes into cells.

Examples: Viral Genomes, Transposons, and Plasmids

question

Techniques of Genetic Engineering:

answer

1. Polymerase Chain Reaction
2. Gel Electrophoresis
3. Southern Blot
4. DNA Microarrays
5. Inserting DNA into Cells

question

What is Polymerase Chain Reaction?

answer

Technique by which scientists produce a large number of identical molecules of DNA in vitro.

question

What is Gel Electrophoresis?

answer

Technique used to isolate fragments of DNA molecules that can be inserted into Vectors.

question

What is Southern Blot?

answer

A method to transfer DNA from agarose gels to nitrocellulose membranes.

question

What are DNA Microarrays?

answer

An array consisting of molecules of single-stranded DNA, which is immobilized on glass slides, silicon chips, or nylon membranes.

question

Three artificial techniques for introducing DNA into cells:

answer

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.

question

Some products produced by recombinant DNA Technology:

answer

Vaccines, DNA fingerprinting, Herbicides

question

Parts of DNA:

answer

Deoxyribose Sugar
Nitrogenous Base
Phosphate Group

question

Eukaryotic Genomes:
Shape -
Contained Within -

answer

Linear Shape
Contained within the nucleus

question

What are nucleosomes?

answer

DNA and Histones wrapped together.

question

What are chromatin fibers?

answer

Nucleosomes clumped together with other proteins.

question

Other than the nucleus where else can Eukaryotic DNA be found?

answer

Within mitochondria or chloroplasts.

question

Define: Gene

answer

Specific sequences of nucleotides that code for polypeptides or RNA molecules.

question

Describe: Base Pairs

answer

The specific way which one of 5 nitrogenous bases are hydrogen bonded to one another.

question

Which base pair are triple bondedWhich are double bonded?

answer

Triple = Guanine and Cytosine
Double = Adenine and Thymine

question

The two strands of DNA are called(Hint: orientation)

answer

Antiparallel

question

Which bacteria have histones?

answer

Archaea

question

Direction of DNA synthesis:

answer

5' to 3' direction

question

Why is DNA replication called semi-conservative?

answer

New DNA is composed of 1 original strand and 1 daughter strand.

question

What is a Heterochromatin?

answer

Closed, inactive DNA

question

What is a Euchromatin?

answer

Open, active DNA.

question

Genetic Recombination:
Transduction and Steps

answer

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.

question

Genetic Recombination:
Transformation

answer

Recipient cell takes up DNA from the environment, such as DNA from dead organisms.

-Mouse Experiment

question

3 Effects of Mutations

answer

Silent Mutation
Missense Mutations
Nonsense Mutations

question

What is a Silent Mutation

answer

No change to amino acid sequence due to redundancy of genetic code.

question

What is a Missense Mutation

answer

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.

question

What is a Nonsense Mutation

answer

Changes an amino acid into a stop codon.

question

Types of Mutations

answer

Point Mutations
Framshift Mutations
Gross Mutations

question

What are point mutations?

answer

One nucleotide base pair is affected.

question

What are frameshift mutations?

answer

When insertions or deletions cause the entire sequence to shift.

question

What are gross mutations?

answer

Large deletions, transpositions, or inversions of genetic sequences.

question

Define: Mutation

answer

A permanent change in the nucleotide base sequence of a genome.

question

What is an Operon?

answer

Section of DNA that includes a promoter, operator, and subsequent genes.

Operon
[----------------------------------------]
{AAAA}{=Promotor=}{=Operator=}{=Gene1=}{=Gene2=}{AAAAAAA}

question

What are triplets?

answer

A sequence of 3 nitrogenous bases.

question

What are codons?

answer

Triplets of mRNA that code for a specific anti-codon or amino acid.

question

What are anti-codons?

answer

Matching base pairs to codons, located on tRNA.

question

What bases are methylated in:
Bacteria
Eukarya

answer

Bacteria: Adenine and rarely Cytosine
Eukarya: Cytosin only.

question

Differences in Eukaryotic and Bacteria DNA replication:

answer

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.

question

4 Types of Eukaryotic Polymerases

answer

Alpha(1) - Initiates
Delta(4) - Elongates Leading Strand
Epsilon(5) - Replicates Lagging Strand
Gamma(3) - Replicates Mitochondrial DNA

question

Bacteria Archaea Eukarya

# Chromo

Plasmids
DNA Shape

DNA Locale

Histones?

answer

|Bacteria | Archea | Eukarya
|___________|___________|_________
# Chromo| Haploid | Haploid | Diploid
|___________|___________|_________
Plasmid?| In some | In Some |FungiPro
|___________|___________|_________
DNA Shp | Circular | Circular | Linear
|___________|___________|_________
DNA Loc | Nucleoid | Nucleoid | Nucleus
| Plasmids | Plasmids | Mitochon
|___________|___________|_________
Histones| No | Yes | Yes
|___________|___________|_________

question

Topoisomerase

answer

Removes supercoils during DNA replication of bacteria, and unwinds DNA for replication in eukaryotes.

question

DNA Ligase

answer

Seals gaps between Okazaki Fragments of lagging strand.

question

RNA Primer (Primase)

answer

Provides 3' hydroxyl group required by DNA polymerase.

question

DNA Polymerase I

answer

Replaces RNA primer w/DNA

question

DNA Polymerase III

answer

The usual enzyme of DNA replication in bacteria and mitochondria.

question

DNA Polymerase

answer

Adds new nucleotides into open DNA strands.

question

DNA Helicase

answer

Breaks hydrogen bonds.

question

Why is one strand of DNA called the 3' strand?

answer

Because it ends with a hydroxyl group bound to the 3' carbon.

question

Why is one strand of DNA called the 5' strand?

answer

Because it ends with a phosphate group attached to the 5' carbon.

question

Roles of Methylation in Bacteria (4)

answer

1. Control genetic expression
2. Initiation of DNA replication
3. Protection against viral infection
4. Repair DNA

question

DNA Replication: Steps (5)
Lagging Strand

answer

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.

question

DNA Replication: Steps (5)
Leading Strand

answer

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.

question

Enzyme responsible for Proofreading Replicated DNA and correcting errors?

answer

Proofreading Exonuclease

question

DNA Replication: Initial Steps (4)

answer

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.

question

Types of Plasmids and their Functions

answer

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.

question

Prokaryotic Genomes:
Where is DNA storedWhere are chromosomes located?

answer

In Chromosomes or plasmids.
Within the nucleoid region.

question

Define: Genome

answer

The entire genetic compliment of a cell or virus. Including its genes and nucleotide sequences.

question

Genetic Recombination: Conjugation (Process)

answer

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.

question

What is gene therapy?

Risks?
Benefits?
Limitations?

answer

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.

question

Human genetic defects targeted by gene therapy.

answer

Cystic Fibrosis
Sickle-cell anemia
Hemophilia
Diabetes

question

What is DNA Fingerprinting

answer

Technique to identify unique sequences of DNA.

question

What are some applications for DNA Fingerprinting?

answer

Paternity Investigations
Crime Scene Forensics
Diagnostic Microbiology
Epidemiology

question

What is "Antisense" DNA Technology?

answer

The technique of using nucleic acid molecules that have nucleotide sequences that bind to and interfere with genes and mRNA molecules.

question

What is a GMO?

answer

Genetically modified organism, used to produce proteins and enzymes not typically found within said organism.

question

Novel properties of Viruses:

answer

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.

question

General size of a virus is measured in?

answer

Nanometers

question

When a virus is outside of a cell it is referred to as a?

answer

Virion

question

All virions have these basic parts:

Some also have:

answer

All: Capsid and a Nucleic Acid Core

Some: Envelope (Phospholipid membrane)

question

The term referring to a capsid and its nucleic acid core is:

answer

Nucleocapsid

question

The outermost layer of a virus, either the capsid or envolope provides these funcitons:

answer

Protection and recognition sites for specific hosts.

question

Define: Capsid

answer

Protein coating surrounding nucleid acid core of a virus.

question

Define: Capsomere

answer

The proteinaceous subunits of a capsid.

question

A virus that infects bacteria is called?

answer

Bacteriophage

question

Name given to viruses that will infect many types of cells in many different hosts.

answer

Generalists

question

Virus is latin for:

answer

Poison

question

Smallest Virus size:

Largest Virus size:

answer

Smallest: 10nm

Largest: 400nm

question

Define: Matrix Protein

answer

Proteins that fill the region between capsid and envelope.

question

Define: Viral Envelope

answer

A membrane located externally to the viral capsid.

question

How does a capsid acquire a viral envelope?

answer

When a virus is released from a host cell it is coated with a portion of the host cells external membrane.

question

In addition to the viral envelope what else does the virus pick up while being exocytosed? What are these used for?

answer

Glycoproteins, used for recognition of like cells.

question

Chemical Composition of Capsomer:

answer

Protein

question

Chemical Composition of Capsid:

answer

Protein

question

Chemical Composition of Viral Genome:

answer

Nucleic Acid

question

Chemical Composition of Viral Envelope:

answer

Phospholipid Bilayer and Proteins

question

Chemical Composition of Viral Spike:

answer

Glycoprotein

question

Five stages of viral replication:

answer

1. Attachment
2. Entry
3. Synthesis
4. Assembly
5. Release

question

Viral Replication: Explain Attachment

answer

Connecting of the virion to a host cell.

question

Viral Replication: Explain Entry

answer

A virion or its genome entering a host cell.

question

Viral Replication: Explain Synthesis

answer

Creation of new nucleic acids and viral proteins by the host cell's enzymes and ribosomes.

question

Viral Replication: Explain Assembly

answer

Building of new virions within the host cell.

question

Viral Replication: Explain Release

answer

Virions leaving the host cell either by lysing or exocytosis.

question

How does lysogenic replication differ from lytic replication?

answer

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.

question

An inactive bacteriophage is called:

answer

Prophage

question

3 Ways animal viruses can penetrate a host cell?

answer

1. Direct Penetration
2. Membrane Fusion
3. Endocytosis

question

Additional step that animal viruses must do after entering host cell:

answer

Uncoating the Capsid.

question

For the genome: dsDNA
How is mRNA synthesizedWhat molecule is template for Genome Replication?

answer

mRNA Synth: RNA Polymerase (in nucleus or cytoplasm)
Molecule: Each strand of DNA serves as template for its compliment.

question

For the genome: ssDNA
How is mRNA synthesizedWhat molecule is template for Genome Replication?

answer

mRNA Synth: RNA polymerase (in nucleus)
Molecule: Complementary strand of DNA is synthesized.

question

For the genome: +ssRNA
How is mRNA synthesizedWhat molecule is template for Genome Replication?

answer

mRNA Synth: Genome acts as mRNA
Molecule: -RNA complementary to the genome is synthesized to act as template.

question

For the genome: +ssRNA (Retroviridae)
How is mRNA synthesizedWhat molecule is template for Genome Replication?

answer

mRNA Synth: DNA from RNA using reverse transcriptase. mRNA is transcribed from DNA by RNA polymerase.
Molecule: DNA

question

For the genome: -ssRNA
How is mRNA synthesizedWhat molecule is template for Genome Replication?

answer

mRNA Synth: RNA dependent RNA transcriptase
Molecule: +mRNA (compliment to viral genome)

question

For the genome: dsRNA
How is mRNA synthesizedWhat molecule is template for Genome Replication?

answer

mRNA Synth: Positive strand of genome acts as mRNA.
Molecule: Each strand acts as template.

question

Steps of Animal Virus Replication: (6)

answer

1. Attachment
2. Penetration
3. Uncoating
4. Synthesis
5. Assembly
6. Release

question

What term describes a nonenveloped virus?

answer

Naked

question

Name given to viruses that shed from host cell slowly and relatively steadily without killing the host cell.

answer

Persistent infections.

question

Two ways naked viruses are released from host cells:

answer

Exocytosis or by cell lysis.

question

Examples of latent viruses:

answer

Herpes and Chicken Pox

question

Define: Lysogenic Conversion

answer

Conversion of a harmless form of bacteria to a pathogenic form.

question

Difference in Latency vs. Lysogeny

answer

In latency the viral DNA does not necessarily become incorporated into the host DNA.

question

Uncontrolled cell division in a multicellular animal is called:

answer

Neoplasia

question

Define: Oncogenes

answer

Active genes that control cell division rate.

question

Factors that contribute to the inhibition of oncogene repressors and the activation of oncogenes:

answer

UV Light
Radiation
Carcinogens
Viruses

question

How are viruses classified?

answer

DNA or RNA strand type.

question

Define: Viroids

answer

Extremely small, circular pieces of RNA that are infectious and pathogenic to plants.

question

Define: Prions

answer

Proteinaceous infective particles.

question

How do Prions infect cells?

answer

By hijacking the cellular membrane protein PrP of the host and converting it to prion PrP.

question

Examples of diseases associated with Prions:

answer

Mad Cow Disease (Bovine Spongiform Encephalitis)
Scrapie in sheep.
Kuru
Chronic Wasting Disease in deer and elk.
Creutzfeldt-Jakob disease in humans.

question

A virus that is specific for a bacterial host is called a:

answer

Phage

question

Name 3 criteria for specific family classification of viruses:

answer

1. Type of nucleic acid.
2. Envelope Structure
3. Capsid Type

question

A clear zone of phage infection in a bacterial lawn is:

answer

A Plaque

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