Exam III Flashcards
List four functions of proteins in cells
- Enzymes that catalyze nearly all chemical reactions in a cell
- Proteins play structural roles acting as the cytoskeleton of cells and as membrane channels that allow molecules or atoms to pass into or out of the cell
- Some toxins made by disease-causing microorganisms are proteins
- Antibiotics made by the human immune system are proteins
Macromolecules that play structural roles acting as the cytoskeleton of cells and as membrane channels that allow molecules or atoms to pass into or out of the cell.
Proteins
Enzymes that catalyze nearly all chemical reactions in a cell are what type of macromolecule?
Proteins
Toxins made by disease-causing microorganisms are what type of macromolecule?
Proteins
Antibiotics made by the human immune system are what type of macromolecule?
Proteins
What type of macromolecule is used as membrane channels?
Protein
Give examples of five functions of proteins in eukaryotes and bacteria.
- Cytoskeleton
- Membrane channels
- Enzymes
- Toxins
- Antibodies
Define a “gene.”
A segment of DNA that codes for a protein or sometimes functional RNA.
What is a segment of DNA that codes for a protein or sometimes functional RNA called?
A gene
Define “gene expression.”
The process of turning the information in a gene into a functional product.
Consists of the processes of transcription and translation.
What is the process of turning the information in a gene into a functional product called?
Gene expression
What process consists of transcription and translation?
Gene expression
What are the two processes involved in gene expression?
Transcription and translation
When DNA is being accessed to code for a protein, what comes first: translation or transcription?
Transcription (“c” comes before “l” in translation)
Define DNA polymerase, focusing on its role in DNA replication.
- DNA polymerase, adds dNTPs to the 3’ end of the newly synthesized DNA chain.
- The dNTP added (either dATP, dTTP, dCTP or dGTP) is the one that base-pairs with the nucleotide on the template strand.
- DNA polymerase pauses every time it adds a nucleotide to double-check if the correct nucleotide is added. If the wrong nucleotide is added, it can “back-space” and cut out the incorrect nucleotide.
What molecules does DNA polymerase adds to the 3’ end of the newly synthesized DNA chain?
dNTPs
What type of protein is DNA polymerase?
An enzyme
What does dNTP stand for?
Deoxynucleotide triphosphate
How many types of dNTPs are there and what are they called?
There are 4 dNTPs:
- dATP (deoxyadenosine triphosphate)
- dCTP (Deoxycytidine triphosphate)
- dTTP (deoxythymidine triphosphate)
- dGTP (deoxyguanosine triphosphate)
What do dNTPs bind with?
dNTPs base-pair with the nucleotide on the DNA template strand as follows:
dATP –> Thymine
dTTP –> Adenine
dCTP –> Guanine
dGTP –> Cytosine
When does DNA polymerase pause?
Each time after it adds a nucleotide.
Why does DNA polymerase pause after each nucleotide added?
To double-check if the correct nucleotide is added.
What does DNA polymerase do if the wrong nucleotide has been added?
DNA polymerase can “back-space” and cut out the incorrect nucleotide.
Does DNA polymerase have a process to prevent the wrong nucleotide from being added to a new strand of DNA?
Yes. DNA polymerase can “back-space” and cut out the incorrect nucleotide.
To which end does DNA polymerase add a nucleotide?
The 3’ end.
How are 3’ and 5’ pronounced?
Three prime and five prime
What does DNA ligase do?
This enzyme repairs small breaks in the phosphate-sugar backbone of DNA. It joints the Okazaki fragments on the lagging strand together.
What type of molecule is DNA ligase?
An enzyme
What enzyme repairs small breaks in the phosphate-sugar backbone of DNA?
DNA ligase
In DNA replication, what enzyme joins the Okazaki fragments on the lagging strand together?
DNA ligase
Define Primase and list its function.
Primase is an enzyme that makes a small RNA molecule that is known as a primer.
DNA polymerase can begin synthesizing DNA by adding dNTPs on the 3’ end of the primer.
What enzyme makes a small RNA molecule that is known as a primer?
Primase
DNA polymerase can begin synthesizing DNA by adding dNTPs on the 3’ end of what?
The primer, a small RNA molecule produced by primase.
How does DNA polymerase begin synthesizing DNA?
By adding dNTPs to the 3” end of the primer produced by primase.
On what end of the primer does DNA polymerase start adding dNTPs?
3’
What does helicase do?
Helicase unwinds the two strands of DNA at the replication fork.
Which enzyme unwinds the two strands of DNA at the replication fork?
Helicase
Where does helicase unwind DNA?
At the replication fork
What is topoisomerase?
The enzyme that releases the tension in the parental DNA molecule caused by unwinding at the replication fork.
What occurs as a result of helicase unwinding the DNA?
The unwinding creates tension in the DNA to come back together.
What is the enzyme that relieves the tension created by helicase?
Topoisomerase
Which strand is the leading strand in DNA synthesis?
The strand that is synthesized continuously.
The 3’ end of the newly-synthesized DNA molecule faces toward the direction the replication fork is opening up in.
Which strand of DNA is synthesized continuously?
The leading strand
What replication characteristic does the leading strand have that the lagging strand does not?
It is replicated continuously.
Also, it replicated at the 3’ end in the direction that the replication fork is opening up to.
What is the lagging strand in DNA synthesis?
The lagging strand is synthesized in short segments called Okazaki fragments.
The 3’ end of the newly-synthezied DNA molecule faces away from the direction that the replication for is opening up to.
What strand of DNA is synthesized in short segments in DNA replication?
The lagging strand
At which end of the DNA molecule does the lagging strand start DNA replication?
The 3’ end
Which strands, the leading or lagging strand starts DNA synthesis at the 3’ end?
Both strands
Which strand in DNA replication moves in a direction away from the direction that the replication fork is moving?
The lagging strand
What are the short segments of DNA synthesized in the lagging strand called?
Okazaki fragments
What are Okazaki fragments?
Short strands of newly synthesized DNA on the lagging strand
What is the origin of replication?
This is a sequence of DNA nucleotides where DNA replication begins.
What is the sequence of nucleotides where DNA replication begins called?
The origin of replication
What is transcription?
Transcription is the process of using the informatoin in a DNA sequence to make an RNA sequence.
What is the process of using the information in a DNA sequence to make an RNA sequence?
Transcription
What does RNA polymerase do?
RNA polymerase is the enzyme that joins NTPs together to form an RNA chain, based on the sequence of a template DNA.
What enzyme joins NTPs together to form an RNA chain, based on the sequence of a template DNA?
RNA polymerase
What is template DNA?
Template DNA is the strand of DNA to which NTPs bind to make the RNA molecule.
The binding of NTPs to the template DNA strand determine the sequence of bases in the RNA molecule.
The binding of NTPs to the template DNA strand determine what in the RNA molecule?
The sequence of bases in the RNA molecule
What is the strand of DNA that NTPs bind to to make RNA?
The template DNA
Match the name to the function of each:
dNTPs NTPs
DNA synthesis RNA synthesis
dNTPs are used in DNA synthesis
NTPs are used in RNA synthesis
What does NTP stand for?
Nucleotide triphosphates (specifically ribonucleotide triphosphate)
What is the abbreviation for ribonucleotide triphosphate and what function do they serve?
NTP. Used in RNA synthesis.
What is the abbreviation of deoxyribonucleotide triphosphate and where does it have a function?
dNTP. Functions in DNA replication.
What do NTPs and dNTPs have in common?
They both act as the building blocks and fuel, the first for RNA synthesis, the second for DNA replication.
What do NTPs do?
NTPs act as the building blocks and the fuel for RNA synthesis.
How do NTPs provide fuel for RNA synthesis?
The removal of two phosphate groups when the NTP is added to the growing RNA chain provides the energy for the reaction.
What is provided when two phosphate groups are removed from the NTP during a growing RNA chain?
Fuel (energy) for the reaction is provided
How many NTPs are there and what are they?
Four NTPs.
There is one for each of the nitrogenous bases found in RNA: ATP, CTP, GTP, UTP.
What are ATP, CTP, GTP and UTP?
NTPs used in RNA synthesis
What is messenger RNA?
mRNA contains a series of codons that correspond to a sequence of amino acids in the protein being made.
It acts as the template in translation.
What does mRNA contain that corresponds to a sequence of amino acids in the protein being made?
Codons
What acts as the template in translation?
mRNA
What does mRNA code for?
Proteins
What is tRNA?
rRNA is the RNA component of the ribosome.
What does rRNA do?
rRNA takes the role of the enzyme in translation, catalyzing the transfer of amino acids from a tRNA to the growing protein chain.
What molecule catalyzes the transfer of amino acids from a tRNA to the growing protein chain?
Ribosomal RNA
What does tRNA do?
Transfer RNA acts as an adaptor between the mRNA and the protein sequence being made.
What is the structure of tRNA?
Each tRNA has an anticodon at one end and a specific amino acid attached to the other end, forming an aminoacyl-tRNA. The anticodon binds to the codon in mRNA and the specific amino acid for which that codon codes is attached to the other end of the tRNA. There is a tRNA for each of the codons in the genetic code chart.
What is attached to each end of a tRNA molecule?
tRNA has an anticodon at one end and a specific amino acid attached to the other end.
This formation is an aminoacyl-tRNA.
Why is a tRNA called an aminoacyl-tRNA?
Because the structure is a tRNA with an amino group at one end and an anticodon at the other.
T/F
There is a tRNA for each of the codons in the genetic code chart.
True
What acts as an adapter between the mRNA and the protein sequence being made?
tRNA
What binds to the codon in mRNA?
The anticodon in tRNA
What do an anticodon and the specific amino acid coded for by mRNA represent?
The two ends of the tRNA molecule
What is translation?
Translation is the process of using the information in an mRNA template to make a protein (sequence of amino acids)
What is the process of using the information in an mRNA template to make a protein (sequence of amino acids)?
Translation
What does mRNA act as in translation?
The template
T/F
The sequence of codons in an mRNA molecule determines the sequence of amino acids in the protein that is made.
True
What determines the sequence of amino acids in the protein that is made?
The sequence of codons in an mRNA
What does the sequence of codons in an mRNA molecule determine?
The sequence of codons in an mRNA molecule determines the amino acids in the protein that is made.
What do aminoacyl-tRNAs do?
They act as monomers that join together to make the protein.
What act as monomers that join together to make a protein?
Aminoacyl-tRNAs
T/F
tRNA does not act as an adaptor molecule.
False
What does it mean that tRNA acts as an adaptor molecule?
It means that tRNA has an anticodon that binds to a a codon on the mRNA sequence which serves to match an amino acid to the codon.
What has an anticodon that binds to the codon on mRNA which serves to match an amino acid to the codon?
tRNA
What occurs when the anticodon of tRNA binds to mRNA?
The amino acid is transferred from the tRNA to the end of the protein chain that is being synthesized.
When is an amino acid transferred from the tRNA to the end of the protein chain that is being synthesized?
After the anticodon of the tRNA binds to the codon on mRNA.
What is a ribosome?
A large RNA-protein complex that acts as the enzyme in translation.
What complex acts as the enzyme in translation?
The ribosome
What catalyzes the chemical reaction that transfers the amino acid that is attached to a tRNA to the end of the protein chain being synthesized?
The ribosome
Where is the bond that links the amino acid to the tRNA broken?
At the ribosome
What results in breaking the bond that links the amino acids to the tRNA?
The ribosome catalyzes the chemical reaction that transfers the amino acid that is attached to a tRNA to the end of the protein chain that is being synthesized.
When a ribosome catalyzes the reaction that transfers the amino acid that is attached to the tRNA to the protein chain, when bonds are broken and which are created?
The bonds linking the amino acid to the tRNA are broken and a peptide bond is formed between amino acids and the protein chain.
When are the bonds linking the amino acid to the tRNA broken and a peptide bond formed between amino acids and the protein chain?
After the ribosome catalyzes the chemical reaction that transfers the amino acid attached to the tRNA to the end of the protein chain that is being synthesized.
What type of bonds are formed between the amino acids being added to the protein chain in translation?
Peptide bonds
Using the chart, fill in the nucleotide sequence of the anticodon and codon for Trp-tRNA
(the amino acid tryptophan attached to a tRNA bound to an mRNA).
Using the genetic code chart, we find that the codon that corresponds to the amino acid TRP is UGG. This will be the codon that is found in the mRNA sequence. The anticodon that is found on the tRNA will be the RNA sequence that binds to UGG, which is ACC. Each codon on the chart would have an aminoacryl-tRNA that has an anticodon that binds to the codon.
e.g. 6 codons code for leucine (Leu):
UUA, UUG, CUU, CUC, CUA and CUG.
6 different aminoacyl-tRNAs with Leu attached, the anticodons that bind to those codons:
AAU, AAC, GAA, GAG, GAU and GAC.)
Describe the summary of events at the DNA replication fork.
- Helicase enzymes unwind the parental double helix.
- Topoisomerase proteins stabilize the unwound parental DNA.
- The leading strand is synthesized continuously from the primer by DNA polymerase.
- The lagging strand is synthesized discontinuously. Primase, an RNA polymerase, synthesizes a short RNA primer, which is then extended by DNA polymerase.
- DNA polymerase digests RNA primer and replaces it with DNA.
- DNA ligase joins the discontinuous fragments (Okazaki fragments) of the lagging strand.
Describe the summary of events in DNA replication.
- Helicase enzymes unwind the parental double helix.
- Topoisomerase proteins stabilize the unwound parental DNA.
- The leading strand is synthesized continuously from the primer by DNA polymerase.
- The lagging strand is synthesized discontinuously. Primase, an RNA polymerase, synthesizes a short RNA primer, which is then extended by DNA polymerase.
- DNA polymerase digests RNA primer and replaces it with DNA.
- DNA ligase joins the discontinuous fragments (Okazaki fragments) of the lagging strand.
What is the result from DNA replication?
Each DNA molecule has one of the parent strands and one newly-made strand.
This is called semiconservative DNA replication.
What is semiconservative DNA replication?
Semiconservative DNA replication means that one of the strands is a parent strand and one is a newly-formed strand in each of the 2 resulting DNA molecules.
Mark the replication fork and the origin of replication.
Check email response from Dr. Suran
What type of replication is DNA replication?
Bidirectional, semi-conservative
What is a missense mutation?
Missense mutations are one of the three types of base substitutions (along with silent: no change in base sequence and nonsense mutations: inserts stop codon in protein sequence) whereby a single-base substitution results in a change in a single amino acid in the entire sequence of the protein.
In a missense mutation, a codon that codes for an amino acid is changed to a codon that codes for a different amino acid.
What type of mutation is a base substitution mutation whereby a single-base substitution results in a change in a single amino acid in the entire sequence of the protein.
Missense mutation
In what type of mutation does a codon that codes for an amino acid get changed to a codon that codes for a different amino acid.
Missense mutation
What is a silent mutation?
A silent mutation is one of the three types of base substitutions whereby a single base is replaced with another but the corresponding codon change corresponds to the same amino acid.
A codon is changed to a different codon that corresponds to the same amino acid.
What type of mutation is one of the three types of base substitutions whereby a single base is replaced with another but the corresponding codon change corresponds to the same amino acid.
Silent mutation
The mutation where a codon is changed to a different codon that corresponds to the same amino acid.
Silent mutation
What type of base substitution changes the sequence in a codon but not the resulting amino acid?
Silent mutation
What type of mutation is a nonsense mutation?
A nonsense mutation is a type of base substitution whereby a stop codon is inserted in a protein chain that stops the addition of amino acids.
No amino acids are added after this codon.
What mutation is a type of base substitution whereby a stop codon is inserted in a protein chain that stops the addition of amino acids.
Nonsense mutation
What mutation results in no amino acids being added after the addition of this codon?
Nonsense mutation
What are the three types of base substitution mutations?
- Missense mutation: a change in the codon that results in the coding of a different amino acid.
- Nonsense mutation: the insertion of a stop code in the sequence that results in no more amino acids added to the chain.
- Silent mutation: a change in the codon that codes for the same amino acid in the chain.
What are the following: Missense mutation, nonsense mutation and silent mutation?
The three types of base substitution mutations
Which mutation makes a change in the codon that results in the coding of a different amino acid?
Missense mutation
What type of mutation inserts a stop code in the sequence that results in no more amino acids added to the chain?
Nonsense mutation
What type of mutation makes a change in the codon that codes for a different amino acid in the chain.
Missense mutation
What type of mutation makes a change in the codon that codes for the same amino acid in the chain.
Silent mutation
What is a frame-shift mutation?
A frameshift mutation is a mutation that does not happen in multiples of three.
This changes the reading frame (where one codon ends and the next begins) downstream of the mutation. This will most likely change all of the amino acids downstream of the mutation and will also likely change the length of the protein.
What is a nonframeshift mutation?
A mutation that occurs in a multiple of three.
Results in an additional amino acid being added to the sequence.
What is the difference between a frameshift mutation and a non-frameshift mutation?
A frameshift mutation does not occur in multiplies of three bases (no one codon) and a non-frameshift mutation occurs in multiples of three (an additional codon).
Which mutation does not occur in multiplies of three bases and which mutation does?
A frameshift mutation does not occur in multiples of three and a non-frameshift mutation occurs in multiples of three.
Which type of mutation occurs in multiples of three and what is the result?
A non-frameshift mutation occurs in multiples of three and results in an additional amino acid added to a sequence.
Which type of mutation does not occur in multiples of three and what is the result?
A frameshift mutation does not occur in multiples of three and the additional base(s) added will shift the sequence to change all the subsequent amino acids in the protein.
What type of mutation will change all the amino acids in the sequence after the point of the mutation?
Frameshift mutation
What type of mutation inserts another amino acid in the protein sequence?
Non-frameshift mutation
What type of mutation is the following and how would it affect the protein sequence if it occured at the 50th codon of a 100 codon chain?
A mutation that changes the codon UCA to UCC
This is a silent mutation because both UCA and UCC code for Serine. If this occured at the 50th codon in a protein made from 100 codons, the new protein would be identical to the original protein.
If a mutation caused both the original codon and the new codon to code for the same protein and the change meant that the new protein sequnence would be identical to the original, what type of mutation would this be?
Silent mutation
What type of mutation is the following and how would it affect the protein sequence if it occured at the 50th codon of a 100 codon chain?
A mutation that changes the codon UCA to UUA
UCA corresponds to Ser and UUA corresponds to Leu so this is a missense mutation.
If this mutation occured at the 50th codon in a protein made from a 100-codon mRNA, the protein made from the mutant mRNA would be identical to one made from the orginal mRNA except for the 50th amino acid which would be Leu instead of Ser.
If a mutation occured at the 50th codon in 100-codon mRNA and the protein made from the mutant mRNA was identical to one made from the orginal except the 50th amino acid was changed from UCA instead of UUA, what type of mutation would this be?
Missense mutation
What type of mutation is the following and how would it affect the protein sequence if it occured at the 50th codon of a 100 codon chain?
A mutation that changes the codon UCA to UAA
UCA corresponds to Ser, UAA is a stop codon. This is a nonsense mutation. If this mutation occurred at the 50th codon in a protein that was made from a 100-codon mRNA, the protein made from the mutant mRNA would be identical to one made from the original mRNA for the first 49 amino acids. At this point the mutant protein would end.
What type of mutation would occurr at the 50th codon in a protein that was made from a 100-codon mRNA, where the protein made from the mutant mRNA would be identical to one made from the original for the first 49 amino acids but at this point the mutant protein would end?
Nonsense mutation because the mutant inserts a stop codon.
What kind of damage is caused by exposure to UV light?
UV light is a mutagen that can cause thymine dimers to form in DNA. In thymine dimers, two neighboring thymine amino acids in the DNA chain chemically react and become covalently bonded to each other. As a result, they cannot pair normally with the opposite strand. The cell can no longer use the top strand for DNA replication or transcription.
How is the damage caused by UV light repaired?
This damage is repaired through excision repair:
- Proteins recognize the deformation of the DNA backbone caused by the thymine dimer.
- An endonuclease cuts out the dimer and some of the surrounding DNA
- The DNA is repaired by a DNA polymerase using the complementary strand as a template
- Ligase seals the nick between the newly-made DNA and the old stand of DNA.
What type of damage is being repaired in the following steps and what is this repair process called?
- Proteins recognize the deformation of the DNA backbone caused by the thymine dimer.
- An endonuclease cuts out the dimer and some of the surrounding DNA
- The DNA is repaired by a DNA polymerase using the complementary strand as a template
- Ligase seals the nick between the newly-made DNA and the old stand of DNA.
This repair process is repairing the damage done by UV light exposure to correct thymine dimers. This is called excision repair.
By what process is the damage caused by UV light exposure repaired?
Excision repair
What are specifically damaged by exposure to UV light?
Neighboring thymine bases
Put the following steps in order for the excision repair process:
- Ligase seals the nick between the newly-made DNA and the old stand of DNA.
- An endonuclease cuts out the dimer and some of the surrounding DNA
- The DNA is repaired by a DNA polymerase using the complementary strand as a template
- Proteins recognize the deformation of the DNA backbone caused by the thymine dimer.
4, 2, 3, 1. The list should be:
- Proteins recognize the deformation of the DNA backbone caused by the thymine dimer.
- An endonuclease cuts out the dimer and some of the surrounding DNA
- The DNA is repaired by a DNA polymerase using the complementary strand as a template
- Ligase seals the nick between the newly-made DNA and the old stand of DNA.
What is the enzyme that excises the dimer caused by a mutagen like UV light?
Endonuclease
What does endonuclease do?
Endonuclease is an enzyme that excises the thymine dimer (and some surrounding DNA) caused by overexposure to UV light.
What enzyme excises the thymine dimer (and some surrounding DNA) caused by overexposure to UV light?
Endonuclease
What enzyme seals the nick between the newly-made DNA and the old strand of DNA after the excision of a thymine dimer and subsequent replacement?
Ligase
What are the enzymes involved in repair after overexposure to UV light?
- Endonuclease (excises the damaged thymine dimers and a bit of surrounding DNA)
- DNA polymerase (repairs the DNA using the complementary strand as a template)
- Ligase (seals the nick bewteen the newl-made DNA and the old strand of DNA)
What process are endonuclease, DNA polymerase and ligase involved in together?
Excision and repair of thymine dimers in skin overexposed to UV light.
What is the Ames test and descibe the procedure used.
The Ames test uses a strain of Salmonella that has a pre-existing mutation that prevents them from synthesizing histidine. These Salmonella require media supplemented with histidine in order to grow, as this amino acid is necessary for making proteins.
To perform the test, a culture of this Salmonella is split in two:
- To one half of the culture, the potential mutagen and rat liver extract is added.
- To the other half of the culture, only the rat liver extract is added.
Both cultures are then plated on histidine-lacking media.
Describe the results that would be seen in the Ames test for both a mutagenic substance and a non-mutagenic substance.
If the substance is mutagenic:
- It will cause mutations in the Salmonella. Some of these mutations will allow the Salmonella to make histidine again. Therefore, there will be more colonies on the experimental plate than on the control plate.
If the substance is not mutagenic:
- It will not cause mutations in the Salmonella. Therefore, there will be the same amount of colonies on the experimental plate as there is on the control plate. Both cultures of Salmonella will experience spontaneous mutations (not caused by the mutagen), so we expect to see colonies on both plates.
This result of the Ames test is an indication of mutagenic or non-mutagenic substance?
It will cause mutations in the Salmonella. Some of these mutations will allow the Salmonella to make histidine again. Therefore, there will be more colonies on the experimental plate than on the control plate.
Mutagenic
Is this result from the Ames test mutagenic or non-mutagenic?
It will not cause mutations in the Salmonella. Therefore, there will be the same amount of colonies on the experimental plate as there is on the control plate. Both cultures of Salmonella will experience spontaneous mutations (not caused by the mutagen), so we expect to see colonies on both plates.
Non-mutagenic
Is this result from the Ames test mutagenic or non-mutagenic?
There will be the same amount of colonies on the experimental plate as there is on the control plate.
Non-mutagenic
Is this result from the Ames test mutagenic or non-mutagenic?
There will be more colonies on the experimental plate than on the control plate.
Mutagenic
Is this result from the Ames test mutagenic or non-mutagenic?
Some of these mutations will allow the Salmonella to make histidine again.
Mutagenic
Is this result from the Ames test mutagenic or non-mutagenic?
We expect to see colonies on both plates.
Non-mutagenic
Briefly describe the difference between regulation by repression and regulation by induction.
There are two types of regulatory proteins: those that add a molecule that turns the gene on are called induction and those that add a molecule to turn the gene off are called repression.
In induction, expression of the gene will turn on in response to a stimulus (usually a specific molecule). Enzymes involved in catabolic pathways are often inducible, which the presence of the molecule to be broken down in the pathway is the stimulus to start gene expression.
In repression, expression of the gene will turn off in response to a stimulus (usually a specific molecule). Enzymes involved in anabolic pathways are often repressible, meaning that the absence of the molecule that the pathway synthesizes is the stimulus to start gene expression.
What are two types of regulatory proteins?
Induction and repression
What does induction mean in the order of regulation by expression?
The presense of a certain molecule or molecules (stimulus) turns gene expression on.
The presense of a certain molecule or molecules (stimulus) that turns gene expression on is called what?
Induction
What does repression mean in the order of regulation by expression?
The presense of a certain molecule or molecules (stimulus) turns gene expression off.
The absense of a certain molecule or molecules (stimulus) that turns gene expression off is called what?
Repression
Enzymes involved in catabolic pathways are often inducible or repressible?
Inducible
Enzymes involved in anabolic pathways are often inducible or repressible?
Repressible
Is the definition below describing induction or repression? Is this indicative of anabolic or catabolic pathways?
The absence of the molecule that the pathway synthesizes is the stimulus to start gene expression.
Repression
Anabolic
Is the definition below describing induction or repression? Is this indicative of anabolic or catabolic pathways?
The presence of the molecule that the pathway synthesizes is the stimulus to start gene expression.
Induction
Catabolism
What is the lac operon?
The lac operon produces enzymes that allow bacteria to catabolize lactose.
What produces enzymes that allow bacteria to catabolize lactose?
The lac operon
Define the function of the following feature of the lac operon: I
lac I: This gene encodes the lac repressor protein. It is constitutively expressed. (Unlike facultative genes that are transcribed only when needed, constitutive genes are expressed continuously.)
Define the function of the following feature of the lac operon: P
lac P: This is not a gene (it does not code for a protein), it is the promoter. This region is the binding site for CAP and RNA polymerase.
Define the function of the following feature of the lac operon: O
lac O: This is not a gene (it does not code for a protein), it is the operator. This is the binding site for the lac repressor protein.
Define the function of the following features of the lac operon structural genes.
lac structural genes: These genes encode the proteins that allow the cell to import and breakdown lactose.
This gene encodes the lac repressor protein. It is constitutively expressed.
lac I
In the lac operon, this is not a gene, it is the promoter.
lac P
In the lac operon, this is not a gene, it is the operator.
lac O
In the lac operon, this region is the binding site for CAP and RNA polymerase.
lac P
In the lac operon, this is the binding site for the lac repressor protein.
lac O
What do the lac P and lac O functions of the lac operon have in common?
- They are not genes (they do not code for proteins).
- They are both binding sites: lac P for CAP and RNA polymerase and lac O for the lac repressor protein
In the lac operon, which features are genes and which are not?
lac I: Gene. Encodes for the lac repressor protein, constitutively expressed.
lac P: Not a gene, is a bindig site for CAP and RNA polymerase
lac O: Not a gene, is a binding site for the lac repressor protein
Structural genes Z, Y, A: Genes. Encode for the proteins that allow the cell to import and breakdown lactose.
State the function name of each:
Gene. Encodes for the lac repressor protein, constitutively expressed.
Not a gene, is a bindig site for CAP and RNA polymerase
Not a gene, is a binding site for the lac repressor protein
Genes. Encode for the proteins that allow the cell to import and breakdown lactose.
lac I: Gene. Encodes for the lac repressor protein, constitutively expressed.
lac P: Not a gene, is a bindig site for CAP and RNA polymerase
lac O: Not a gene, is a binding site for the lac repressor protein
Structural genes Z, Y, A: Genes. Encode for the proteins that allow the cell to import and breakdown lactose.
State the function name:
Gene. Encodes for the lac repressor protein, constitutively expressed.
lac I
State the name of this function of the lac operon:
Not a gene, is a binding site for CAP and RNA polymerase
lac P
State the name of this function of the lac operon:
Not a gene, is a binding site for the lac repressor protein
lac O
State the name of this function of the lac operon:
Genes. Encode for the proteins that allow the cell to import and breakdown lactose.
Structural genes Z, Y, A
State the name of each function the lac operon:
- Genes. Encode for the proteins that allow the cell to import and breakdown lactose.
- Gene. Encodes for the lac repressor protein, constitutively expressed.
- Not a gene, is a binding site for the lac repressor protein
- Not a gene, is a bindig site for CAP and RNA polymerase
- Structural genes, Z, Y, A: Genes. Encode for the proteins that allow the cell to import and breakdown lactose.
- lac I: Gene. Encodes for the lac repressor protein, constitutively expressed.
- lac O: Not a gene, is a binding site for the lac repressor protein
- lac P: Not a gene, is a binding site for CAP and RNA polymerase
When does lac repressor bind to DNA and what sugar does it respond to?
When does lac repressor bind to DNA (when lactose is absent) and what sugar does it respond to (lactose).
Where does lac repressor bind to DNA and what region of the lac operon does it bind to?
Where does lac repressor bind to DNA (the O region) and what region of the lac operon does it bind to (the operator region)?
What effect does the lac repressor binding to DNA have on transcription of the structural genes?
The lac repressor protein blocks transcription of the structural genes when it is bound to the O region.
When does CAP bind to DNA and what sugar does it respond to?
When does CAP bind to DNA (in the absence of glucose) and what sugar does it respond to (glucose)?
Where does CAP bind to DNA and what region of the lac operon does it bind to?
Where does CAP bind to DNA (the P region) and what region of the lac operon does it bind to (the promoter region)?
What effect does CAP have on transcription of the structural genes when bound to DNA?
When bound to the P region, CAP recruits RNA polymerase to the promotor to allow transcription of the lac structural genes.
Complete the boxes to determine the state of the lac repressor protein, CAP, and if there will be transcription of the lac structural genes based on the presence (+) or absence (-) of glucose and lactose.
In the presence of glucose, is CAP bound to the promotor region on DNA?
No
Complete the boxes to determine the state of the lac repressor protein, CAP, and if there will be transcription of the lac structural genes based on the presence (+) or absence (-) of glucose and lactose.
In the absence of glucose, is CAP bound to the promotor region on DNA?
Yes
Complete the boxes to determine the state of the lac repressor protein, CAP, and if there will be transcription of the lac structural genes based on the presence (+) or absence (-) of glucose and lactose.
In the presence of glucose and the absence of lactose, is lac repressor protein bound to operator region on DNA?
Yes
Complete the boxes to determine the state of the lac repressor protein, CAP, and if there will be transcription of the lac structural genes based on the presence (+) or absence (-) of glucose and lactose.
In the presence of glucose and the presence of lactose, is lac repressor protein bound to operator region on DNA?
No
Complete the boxes to determine the state of the lac repressor protein, CAP, and if there will be transcription of the lac structural genes based on the presence (+) or absence (-) of glucose and lactose.
In the absence of glucose and the absence of lactose, is lac repressor protein bound to operator region on DNA?
Yes
Complete the boxes to determine the state of the lac repressor protein, CAP, and if there will be transcription of the lac structural genes based on the presence (+) or absence (-) of glucose and lactose.
In the absence of glucose and the presence of lactose, is lac repressor protein bound to operator region on DNA?
No
Complete the boxes to determine the state of the lac repressor protein, CAP, and if there will be transcription of the lac structural genes based on the presence (+) or absence (-) of glucose and lactose.
In the presence of glucose and the absence of lactose, will transcription of lac structural genes (Z, Y, A) occur?
No
Complete the boxes to determine the state of the lac repressor protein, CAP, and if there will be transcription of the lac structural genes based on the presence (+) or absence (-) of glucose and lactose.
In the presence of glucose and the presence of lactose, will transcription of lac structural genes (Z, Y, A) occur?
No
Complete the boxes to determine the state of the lac repressor protein, CAP, and if there will be transcription of the lac structural genes based on the presence (+) or absence (-) of glucose and lactose.
In the avsence of glucose and the absence of lactose, will transcription of lac structural genes (Z, Y, A) occur?
No
Complete the boxes to determine the state of the lac repressor protein, CAP, and if there will be transcription of the lac structural genes based on the presence (+) or absence (-) of glucose and lactose.
In the absence of glucose and the presence of lactose, will transcription of lac structural genes (Z, Y, A) occur?
Yes
How is the trp operon regulated?
The trp repressor protein is active when bound to tryptophan.
The trp repressor protein is active when bound to what?
Tryptophan
When active, the repressor protein binds to the operator region of the trp operon and affects transcription how?
Prevents transcription
In the absence of tryptophan, what does the repressor protein do?
The repressor does not bind to the O region and transcription can occur.
The trp repressor does not bind to the O region and transcription can occur when what conditions are met?
In the absence of tryptophan
When does the repressor protein bind to the operator region of the trp operon and prevent transcription?
When it is active
The genes of the trp operon are only expressed when the cell needs to make tryptophan when tryptophan concentrations are low. This is an example of an operon governed by induction or repression?
Repression
When are the genes of the trp operon are expressed?
Only when the cell needs to make tryptophan when tryptophan concentrations are low.
The cell needs to make tryptophan when what condition applies?
When tryptophan concentrations are low.
What is transformation?
Transformation is a type of horizontal gene transfer where cells take up naked DNA from the environment around them. Naked DNA is DNA that is free in the environment, as opposed to DNA that is inside another bacterial cell (transferred through conjugation) or in a viral particle (transferred thorugh transduction).
A type of horizontal gene transfer where cells take up naked DNA from the environment around them.
Transformation
What is naked DNA?
Naked DNA is DNA that is free in the environment, as opposed to DNA that is inside another bacterial cell (transferred through conjugation) or in a viral particle (transferred thorugh transduction).
A type of horizontal gene transfer where DNA that is inside a bacterial cell is transferred to another cell.
Conjugation
What is transduction?
A type of horizontal gene transfer where a virus transfers genetic material from one bacterium to another.
What are three mechanisms of horizontal gene transfer in bacteria?
Transformation, transduction, and conjugation.
Describe Frederick Griffith’s experiment that demonstrated transformation.
Griffith had two different strains of Streptococcus pneumoniae, an encapsulated form that grew in smooth colonies on petri dishes (S) and an unencapsulated form that grew in rough colonies on petri dishes (R). The S form was much more virulent (able to cause disease) than the R form, due to the capsule. Griffith tested four different preparations by injecting them into mice:
Preparation injected: Living encapsulated (S) S. pneumoniae,
Result: mouse died
Isolated from mouse after injection: encapsulated (S) S. pneumoniae
Preparation injected: Living unencapsulated (R) S. pneumoniae
Result: mouse lived
Isolated from mouse after injection: Unencapsulated (R) S. pneumoniae.
Preparation injected: Heat-killed encapsulated (S) S. pneumoniae
Result: mouse lived
Isolated from mouse after injection: Nothing
Preparation injected: Mixture of heat-killed encapsulated (S) S. pneumoniae and living unencapsulated (R) S. pneumoniae
Result: mouse died
Isolated from mouse after injection: Encapsulated (S) S. pneumoniae.
Transformation, transduction, and conjugation.
The three mechanisms of horizontal gene transfer in bacteria.
What type of horizontal gene transfer did Frederick Griffith’s S. pneumoniae experiment demonstrate?
This experiment demonstrated transformation. In the fourth preparation, some of the living unencapsultate (R) S. pneumoniae picked up DNA from the heat-killed encapsulated (S) S. pneumoniae that allowed them to make a capsule. This converted the unencapsulated (R) S. pneumoniae into encapsulated (S) S. pneumoniae which allowed them to cause disease.
Who demonstrated the concept of transformation with an experiment using mice and S. pneumoniae?
Frederick Griffith
What are the four preparations injected into mice in Frederick Griffith’s experiment on transformation?
- Living encapsulated (S) S. pneumoniae
- Living unencapsulated (R) S. pneumoniae
- Heat-killed encapsulated (S) S. pneumoniae
- A mixture of heat-killed encapsulated (S) S. pneumoniae and living unencapsulated (R) S. pneumoniae
What were the results of the four preparations injected into mice in Frederick Griffith’s transformation demonstration?
- Living encapsulated (S) S. pneumoniae - mice died
- Living unencapsulated (R) S. pneumoniae - mice lived
- Heat-killed encapsulated (S) S. pneumoniae - mice lived
- A mixture of heat-killed encapsulated (S) S. pneumoniae and living unencapsulated (R) S. pneumoniae - mice died
What was isolated from the mice in the four parts of Frederick Griffith’s transformation demonstration?
- Living encapsulated (S) S. pneumoniae - mice died - Encapsulated (S) - S. pneumoniae
- Living unencapsulated (R) S. pneumoniae - mice lived - Unencapsulated (R) S. pneumoniae
- Heat-killed encapsulated (S) S. pneumoniae - mice lived - Nothing
- A mixture of heat-killed encapsulated (S) S. pneumoniae and living unencapsulated (R) S. pneumoniae - mice died - Encapsulated (S) S. pneumoniae
Describe conjugation
Conjugation occurs when DNA is transferred from one bacterium to another through a sex pilus. The ability to transfer DNA via conjugation is carried by a plasmid known as the F factor (Fertility factor).
Occurs when DNA is transferred from one bacterium to another through a sex pilus.
Conjugation
The ability to transfer DNA via conjugation is carried by what known as the F factor (Fertility factor).
A plasmid
The ability to transfer DNA via conjugation is carried by a plasmid known as ________.
F factor (Fertility factor).
What type of horizontal gene transfer uses a plasmid and the F factor and how is the genetic material transfered?
Conjugation, sex pilus
What are the two mating factor types in conjugation?
F+ and F- cells (Fertility factor cells)
What are F+ and F- cells?
Two types of Fertility factor cells in conjugation.
Define F+ and F- cells used on conjugation.
F+ cells: Contain the plasmid and are able to initate mating
F- cells: Lack the plasmid and are unable to initiate mating
What is the difference between F+ and F- cells used in conjugation?
F+ cells: Contain the plasmid and are able to initate mating
F- cells: Lack the plasmid and are unable to initiate mating
What sometimes happens to the plasmid of the F+ cells and the cell genome?
Sometimes the F+ cell plasmid becomes integrated into the cell genome (cell’s genetic material).
What happens when the F+ plasmid becomes integrated into the cell genome?
These cells become high frequency recombination cells (Hfr). Since the F factor is now on the chromosome of the Hfr cell, parts of the F+ cell chromosome are transferred to the F- cell.
What plasmids have significance importance in medical seettings?
Resistance (R) factors
Why do R factors have important significance in medicine?
Resistance (R) factors carry genes that confer resistance to antibiotics, heavy metals, or cellular toxins to their host (referred to as R-determinates) in addition to the genes normally found on the F factor plasmid that are involved in transferring the plasmid (resistence transfer factors or RTFs).
What are R-determinates?
R-determinates are genes that confer resistance to antibiotics, heavy metals, or cellular toxins to their host that are carried by Resistance (R) factors. These are in addition to RTFs (resistance transfer factor).
What are RTFs found on the F factor plasmid?
RTFs are the genes normally found on the F factor plasmid that are involved in transferring the plasmid (resistence transfer factors or RTFs). They are found in addition to R-determinates that confer resistance to antibiotics, heavy metals, or cellular toxins to their host that are carried by Resistance (R) factors.
Describe the medical significance of F factor plasmid when it becomes integrated into the cell genome as far as R factors and RTFs.
Resistance (R) factors on the plasmid carry genes that confer resistance to antibiotics, heavy metals, or cellular toxins to their host (referred to as R-determinates) in addition to the genes normally found on the F factor plasmid that are involved in transferring the plasmid (resistence transfer factors or RTFs)
What is carried on F plasmids?
- Resistance (R) factors on the plasmid carry genes that confer resistance to antibiotics, heavy metals, or cellular toxins to their host (referred to as R-determinates)
- Genes normally found on the F factor plasmid that are involved in transferring the plasmid (resistence transfer factors or RTFs)
What are R factors?
Resistance (R) factors on the F plasmid carry genes that confer resistance to antibiotics, heavy metals, or cellular toxins to their host (referred to as R-determinates).
What are R-determinates?
Resistance (R) factors on the plasmid carry genes that confer resistance to antibiotics, heavy metals, or cellular toxins to their host (referred to as R-determinates).
What are the genes normally involved in transferring the F factor plasmid?
Resistence transfer factors (RTFs)
What is transduction?
Transduction is the transfer of DNA from a donor cell to a recipient cell via a phage (a bacterial virus) intermediary.
What is a phage?
A bacterial virus intermediary that is responsible for the transfer of DNA from a donor cell to a recipient cell in transduction.
What is the simplest form of transduction?
The simplest form of transduction involves DNA from one host cell being aberrantly packaged into a viral particle and being introduced to another host cell by the viral particle via the mechanisms used to infect cells.
The DNA from the first cell can recombine with the chromosome of the second cell. Once the new DNA is intergrated, it will be passed on to the decendents of the second cell when it divides.
List an example of a substance that is produced by genetic engineering.
- Human Growth Hormone is an example of a protein produced by genetic engineering
- Commercially available restriction enzymes and other enzmes (taq)
- Insulin
- Monoclonal antibodies used for anti-COVID infusions
- Lactases used to make lactose-free milk
What are the two steps to the simplest form of transduction?
The simplest form of transduction involves:
- DNA from one host cell being aberrantly packaged into a viral particle and being introduced to another host cell by the viral particle via the mechanisms used to infect cells.
- The DNA from the first cell can recombine with the chromosome of the second cell. Once the new DNA is intergrated, it will be passed on to the decendents of the second cell when it divides.
What are the following?
- Human Growth Hormone
- Commercially available restriction enzymes and other enzmes (taq)
- Insulin
- Monoclonal antibodies used for anti-COVID infusions
- Lactases used to make lactose-free milk
Substances produced by genetic engineering.
Describe restriction enzymes and how they can be used to isolate a gene of interest from the surrounding DNA.
Restriction enzymes are enzymes that make double-stranded cuts in DNA at specific sequences. Specific restriction enzymes can be chosen that recognize sites on either side of the gene of interest. Digestion of the DNA with the restriction enzymes will separate the gene of interest from the surrounding DNA.
What are enzymes that make double-stranded cuts in DNA at specific sequences?
Restriction enzymes
____________ are enzymes that make double-stranded cuts in DNA at specific sequences.
Specific restriction enzymes can be chosen that recognize sites on either side of the ______ __ ________.
Digestion of the DNA with the restriction enzymes will separate the ____ __ ________ from the surrounding DNA.
Restriction enzymes
gene of interest
gene of interest
Describe the Polymerase Chain Reaction (PCR)
PCR is capable of amplifying a specific sequence of DNA. It uses primers that bind to DNA sequences that flank the gene of interest and amplify it with taq polymerase to the point where it vastly outnumbers the other DNA in the sample.
How does PCR isolate a gene of interest from the surrounding DNA?
PCR uses primers that bind to DNA sequences that flank the gene of interest and amplify it with taq polymerase to the point where it vastly outnumbers the other DNA in the sample.
What are vectors?
Vectors are pieces of DNA used to propagate recombinant DNA in a cell.
What are pieces of DNA used to propagate recombinant DNA in a cell?
vectors
Name two types of vectors.
Two types of vectors:
- Plasmids are circular pieces of DNA based on plasmids found “in the wild” in bacteria and some eukaryotes.
- Viral vectors accept a larger piece of DNA than plasmids. They insert the selected gene into the host cell genome thorugh mechanisms that are part of the unmodified viruses’ life cycle.
Plasmids and viral vectors are two types of what?
Vectors
What are used to propagate recombinant DNA in a cell?
Vectors
Describe how DNA vectors containing recombinant DNA sequences (gene of interest) are made.
- Restriction enzymes are used to cut a vector and the recombinant DNA sequence.
- The vector and the recombinant DNA sequence are joined together by ligase.
- The ligated DNA is then transformed into a bacterial cell, where the origin of replication allows the plasmid to be reproduced and amplified.
- The selectable markers allow one to discriminate between bacterial cells that have taken up the plasmid and those that have not.
- Once a colony of bacteria that contains the recombinant plasmid is isolated, many more of those cells can be grown, all of which contain the plasmid.
- From this large pool of cells, one can isolate a large amount of the recombinant plasmid.
What is the role of restriction enzymes in recombinant DNA?
Restriction enzymes are used to cut a vector and the recombinant DNA sequence.
What is the role of the origin of replication in recombinant DNA?
The origin of replication allows the plasmid to be reproduced and amplified.
What is the role of ligase in recombinant DNA?
Restriction enzymes are used to cut a vector and the recombinant DNA sequence.
The vector and the recombinant DNA sequence are joined together by ligase.
What is the role of selectable markers in recombinant DNA?
Selectable markers allow discrimination between bacterial cells that have taken up the plasmid and those that have not.
Describe how DNA vectors are introduced into host cells by transformation.
Transformation is when cells take up naked DNA from solution. Transformation is commonly used with bacteria and some simple eukaryotes (such as yeasts). Competency refers to the ability of the cell to take up DNA through transformation. Some bacteria naturally take up DNA and are called naturally competnent. Some cells require chemical treatments to allow them to be transformed. After the chemical treament, these cells are referred to as chemically competent. Electroporation is another transformation technique. An electric field makes holes in the cell membrane, allowing the DNA entry to the cell.
What is transformation?
Transformation is when cells take up naked DNA from solution.
Transformation is commonly used with what types of organisms?
Bacteria and some simple eukaryotes (such as yeasts).
What does competency refer to?
Competency refers to the ability of the cell to take up DNA through transformation.
What are the bacteria called that naturally take up DNA?
Some bacteria naturally take up DNA and are called naturally competent.
What are chemically competent cells?
Cells that require chemical treatments to allow them to be transformed.
What are chemically competent cells?
Cells that require chemical treatments to allow them to be transformed. After the chemical treament, these cells are referred to as chemically competent.
What is a method to make cells chemically competent?
Electroporation is a transformation technique where an electric field makes holes in the cell membrane, allowing the DNA entry to the cell.
What are four examples of how DNA vectors are introduced into host cells?
- Transformation
- Microinjection
- Ballistic transformation
- Agrobacterium
What is microinjection?
A solution containing the recombinant DNA is injected into the cell with a very fine glass needle. Microinjection is most commonly used with animal cells, due to their large size and lack of cell wall.
Why is microinjection most commonly used with animal cells?
Due to their large size and lack of cell wall.
What is ballistic transformation?
A technique in making recombinant DNA whereby microscopic particles are coated with DNA and are shot at plant tissue. This technique is primarily used with plant cells.
With what type of cells is ballistic transformation primarily used?
Plant cells
What is the process of Agrobacterium as a DNA recombinant transformation technique?
Agrobacterium transformation is another technique that is primarily used with plants. It naturally contains a plasmid called the Ti plasmid. This plasmid contains a gene called the T-DNA that causes the formation of crown galls when Agrobacterium cells inject the Ti plasmid into plant cells.
To introduce a specific gene into cells, the T-DNA of the Ti plasmid is replaced by a gene of interest. The agrobacterium are then transformed with this plasmid and then the Agrobacterium transfers the DNA to the plant cells. Plant cells that have taken up the DNA are selected for and then grown into full plants.
What is the plasmid in agrobacterium that assists with transformation?
Agrobacterium naturally contains a plasmid called the Ti plasmid. This plasmid contains a gene called the T-DNA that causes the formation of crown galls when Agrobacterium cells inject the Ti plasmid into plant cells.
What gene does the plasmid in agrobacterium use that causes the formation of crown galls when agrobacteirum cells inject the Ti plasmid into plant cells?
Agrobacterium naturally contains a plasmid called the Ti plasmid that contains a gene called the T-DNA that causes the formation of crown galls when agrobacterium cells inject the Ti plasmid into plant cells.
What does the T-DNA of the Ti plasmid in agrobacterium do to introduce a specific gene into cells?
To introduce a specific gene into cells, the T-DNA of the Ti plasmid is replaced by a gene of interest. The agrobacterium are then transformed with this plasmid and then the agrobacterium transfers the DNA to the plant cells. Plant cells that have taken up the DNA are selected for and then grown into full plants.
What bacterium uses transformation to modify via recombinant DNA via Ti plasmid?
Agrobacterium
The natural plasmid in agrobacterium responsible for transformation.
Ti plasmid. This plasmid contains a gene called the T-DNA that causes the formation of crown galls when Agrobacterium cells inject the Ti plasmid into plant cells.
The gene on the Ti plasmid in agrobacterium that is replaced in transformation.
T-DNA. To introduce a specific gene into cells, the T-DNA of the Ti plasmid is replaced by a gene of interest.
What does the gene on the agrobacterium plasmid cause the formation of when injected into the plant cell?
This plasmid contains a gene called the T-DNA that causes the formation of crown galls when agrobacterium cells inject the Ti plasmid into plant cells.
When does the T-DNA gene on the Ti plasmid of agrobacerium cause the formation of crown galls?
When Agrobacterium cells inject the Ti plasmid into plant cells.
What does the T-DNA of the Ti plasmid of the agrobacterium do to introduce a specific gene into cells?
To introduce a specific gene into cells, the T-DNA of the Ti plasmid is replaced by a gene of interest. The agrobacterium are then transformed with this plasmid and then the Agrobacterium transfers the DNA to the plant cells. Plant cells that have taken up the DNA are selected for and then grown into full plants.
Compare viruses and bacteria with respect to:
- Size
- How many types of nucleic acids
- Ribosomes presence
- ATP-generating metabolism
- Antibiotic sensitivities
- Size: Viruses are generally smaller than bacterial cells, ranging from a few nm to nearly 1 um in length.
- Viruses only contain one type of nucleic acid, while bacteria contain both RNA and DNA
- Viruses do not contain ribosomes, they use the ribosomes of their host, while bacteria do contain and make their own ribosomes.
- Viruses do not have their own ATP-generating metabolism, they use the ATP of their host, while bacteria make their own ATP.
- Viruses are not sensitive to antibiotics while bacteria are
How do viruses and bacteria differ in size?
Viruses are generally smaller than bacterial cells, ranging from a few nm to nearly 1 um in length.
How do viruses and bacteria differ in nucleic acids?
Viruses only contain one type of nucleic acid, while bacteria contain both RNA and DNA.
How do viruses and bacteria differ in ribosomes?
Viruses do not contain ribosomes, they use the ribosomes of their host, while bacteria do contain and make their own ribosomes.
How do viruses and bacteria differ in ATP-generation?
Viruses do not have their own ATP-generating metabolism, they use the ATP of their host, while bacteria make their own ATP.
How do viruses and antibiotics differ in antibiotic sensitivity?
Viruses are not sensitive to antibiotics while bacteria are.
What is a helical-shaped virus?
A virus shape the resembles a long rod that may be rigid or flexible. The viral nucleic acid of helical viruses is found within a hollow, cylindrical capsid that has a helical structure.
What is a polyhedral virus shape?
A polyhedral virus has a many-sided capsid. Most polyhedral viruses are isocahedrons which are polyhedrons with 20 triangular faces and 12 corners.
How many triangular faces and corners does an icosahedron have?
20 triangular faces and 12 corners.
Which type of polyhedral are most viruses?
Icosahedron (20 triangular faces and 12 corners)
What is an enveloped virus?
Enveloped viruses have a capsid that is covered by an envelope, which makes all enveloped viruses roughly spherical.
The envelope is most commonly composed of lipids, but many also contain proteins and carbohydrates. Underneath the envelope, the capsid may have a helical or polyhedral arrangement, however the virus is still classified as an enveloped virus.
Enveloped viruses have a capsid that is covered by an envelope, which makes all enveloped viruses roughly what type of shape?
Spherical.
What are most enveloped viruses composed of?
The envelope is most commonly composed of lipids, but many also contain proteins and carbohydrates.
Underneath the envelope, the capsid may have a helical or polyhedral arrangement, however the virus is still classified as what?
An enveloped virus.
What are complex viruses?
Complex viruses are viruses that have more complicated structures than helical, polyhedral or enveloped viruses. Examples include bacteriophages and poxviruses.
Bateriophages have a polyhedral head that contains the viral nucleic acid, a helical tail sheath, and has other structures including a base plate and tail fibers.
Poxviruses have irregular structures. They do not contain a clearly identifiable capsid structure but have several structural coats surrounding their nucleic acid.
What are the shape characteristics of bateriophages?
Bateriophages have a polyhedral head that contains the viral nucleic acid, a helical tail sheath, and has other structures including a base plate and tail fibers.
What shape characteristics are poxviruses?
Poxviruses have irregular structures. They do not contain a clearly identifiable capsid structure but have several structural coats surrounding their nucleic acid.
What do poxviruses have around their nucleic acid?
Several structural coats surrounding their nucleic acid.
Poxviruses do not contain a clearly identifiable what?
They do not contain a clearly identifiable capsid structure.
What shape of virus has a polyhedral head that contains the viral nucleic acid, a helical tail sheath, and has other structures including a base plate and tail fibers?
Bateriophages
What type of viruses have more complicated structures than helical, polyhedral or enveloped viruses?
Complex viruses
What type of complex viruses have irregular structures that do not contain a clearly identifiable capsid structure but have several structual coasts surrounding their nucleic acid?
Poxviruses have irregular structures. They do not contain a clearly identifiable capsid structure but have several structural coats surrounding their nucleic acid.
Describe the structure of a viral capsid.
A capsid is a protein coat that surrounds and protects the nucleic acid.
What is a protein coat that surrounds and protects the nucleic acid of a virus?
A capsid
What is a viral capsomere?
A capsomere is a generic term for the protein subunits that make up the capsid. In some viruses, capsomeres are all the same protein, in others, capsomeres are several different proteins.
What is a generic term for the protein subunits that make up the capsid?
Capsomeres
What are the nucleic acids in viruses?
Viruses can have either DNA or RNA as a genetic material but never both. Depending on the type of virus, the nucleic acid can be double-stranded or single-stranded, can either be linear or circular, can be one piece of nucleic acid or can be multiple pieces.
Viruses can have DNA or RNA, both or either?
Viruses can have either DNA or RNA as a genetic material but never both.
Depending on the type of virus, the nucleic acid can be how many strands?
Depending on the type of virus, the nucleic acid can be double-stranded or single-stranded, can either be linear or circular, can be one piece of nucleic acid or can be multiple pieces.
What is an envelope in regard to a virus?
An envelope is a structure that coats the capsid. It is only found in some viruses. It can consist of a combination of different molecules that can include lipids, proteins and carbohydrates.
Envelopes are found in some viruses or all viruses?
Envelopes are only found in some viruses. They can consist of a combination of different molecules that can include lipids, proteins and carbohydrates.
Envelopes are composed of what macromolecules?
Envelopes can consist of a combination of different molecules that can include lipids, proteins and carbohydrates.
What are spikes in a virus?
Spikes are carbohydrates-protein complexes that project from the surface of the viral particles. They are only found on some viruses and because of this, they can be used as a way of identifying viruses. Spikes are used by some viruses to attach to the host cell.
What are the micromolecules in virus spikes?
Spikes are carbohydrates-protein complexes
Spikes are on
all or some viruses?
Some
Because spikes are found on some viral particles, they can be used for what?
Viral identification
What is the protein coat that sourrounds and protects the nucleic acid of a virus?
A capsid
What is the structure that coats the capsid that is only found in some viruses?
The envelope
Envelopes differ from virus spikes in macromolecule construction how?
Envelopes have carbs, proteins and lipids
Spikes are composed of carbs and proteins
Name the seven types of nucleic acid and replication strategies found in viruses.
Double-stranded DNA
Single-stranded DNA
DNA genome using reverse transcriptase
Double-stranded RNA
Single-stranded RNA, + strand
Singe-stranded RNA, - strand
RNA genome using reverse transcriptase
What are these?
Double-stranded DNA
Single-stranded DNA
DNA genome using reverse transcriptase
Double-stranded RNA
Single-stranded RNA, + strand
Singe-stranded RNA, - strand
RNA genome using reverse transcriptase
Seven types of nucleic acid and replication strategies in viruses.
Describe the criteria used to classify viruses.
Classifications:
- Nucleic acid type
- Strategy for replication
- Morphology of particle
List the criteria to name viruses
Nomenclature:
Suffixes
The suffix -virus is used for genus names
The suffix -viridae is used for family names
The suffix -ales is used for order names.
Family: Herpesviridae, genus: Simplexvirus, human herpesvirus2
A viral species is a group of viruses sharing the same genetic information and ecological niche (host range). Specific epithets for viruses are not used, viruses only have commn names.
The suffix -virus is used for genus, family or order names?
genus
The suffix -viridae is used for genus, family or order names?
Family
The suffix -ales is used for genus, family or order names?
Order
Genus suffix for viruses
-virus
Family suffix for viruses
-viridae
Order suffix for viruses
-ales
What is a bacteriophage?
- Bacteriophages are a type of complex virus with complicated structures moreso than helical, polyhedral or enveloped viruses.
- Bacteriophages have a polyhedral head.
- The head contains the viral nucleic acid.
- It also has a helical tail sheath and has other structures including a base plate and tail fibers.
What is a method of growing bacteriophages in the laboratory?
The plaque method
What is the plaque method?
A method of growing bacteriophages in the laboratory.
Explain the plague method.
The plaque method:
- Agar containing the bacteriophages and host bacteria are poured onto a petri plate containing a hardened layer of agar
- The virus-bacteria mixture solidifies into a thin top layer. The bacteria form a layer about one bacterial cell thick
- Each bacteriophage infects a bacterium, multiplies, and releases several hundred new bacteriophage. These bacteriophage can then infect new cells.
- After several cycles, all of the bacteria in an area are destroyed, which produces a clearing. These clear areas are called plaques
- Each plaque theoretically corresponds to a single bacteriophage
- Concentrations of phage are measured in plaque forming units (PFU), in a similar way to how concentrations of bacterial cultures can be measured in colony forming units (CFU) using the standard plate count.
What are produced in the plaque method of growing bacteriophages in the laboratory?
Concentrations of phage are measured in plaque forming units (PFU), in a similar way to how concentrations of bacterial cultures can be measured in colony forming units (CFU) using the standard plate count.
What does a plaque grown with the plaque method correspond to?
Each plaque theoretically corresponds to a single bacteriophage.
What are three ways of growing animal viruses in the laboratory?
In living animals.
In embryonated eggs.
In cell cultures.
Describe the method of growing animal viruses in the lab by using live animals.
- Some viruses can only be grown in animals.
- Inoculated animals are observed until they show symptoms of infection
- The infected tissues can be analyzed or harvested.
- Some human viruses are unable to infect other animals or show no symptoms in other animals.
Describe the method of growing animal viruses in embryonated eggs.
- A viral suspension or suspected virus-containing tissue is injected into the egg.
- The virus is injected near the region most appropriate for its growth.
- Viral growth is signaled by either the death of the embryo, embryo cell damage, or formation of pocks or lesions in the egg membranes.
- This method is still used to grow viruses for some vaccines (and is why there is monitoring of people with egg allergies after the administration of some vaccines).
Describe the method of growing animal viruses in lab cultures.
- Cell cultures are cells grown in culture media in the laboratory.
- Cell cultures are made by treating a sample of tissue with enzymes that break down the molecules that hold the tissue together
- These cells are grown in Petri dishes in a solution that is the correct osmotic pressure and contains nutrients and growth factors.
- The cells are allowed to replicate in the Petri dish and are then infected with the desired virus.
- After the virus is allowed to infect and replicate in the cells in the culture, it can be harvested from the cell culture media.
Which method of growing animal viruses in the laboratory involves the use of Petri dishes?
Cell cultures
Which method of growing animal viruses in the laboratory results in death of the embryo, embryo cell damage, or formation of pocks or lesions in the egg membranes.
In embronated eggs
Inoculated animals are observed until they show symptoms of infection is a type of what?
Method of growing animal viruses in the laboratory.
What is the difference between lystic and lysogenic cycles?
- The lytic cycle involves the reproduction of viruses using a host cell to manufacture more viruses; the viruses then burst out of the cell.
- The lysogenic cycle involves the incorporation of the viral genome into the host cell genome, infecting it from within.
Which cycle in viral reproduction uses a host cell to manufacture more viruses; the viruses then burst out of the cell.
The lytic cycle
Which cycle in viral reproduction involves the incorporation of the viral genome into the host cell genome, infecting it from within?
The lysogenic cycle
What is a T-even phage?
A good example of a well-characterized class of virulent phages that normally lead to the death of the host cell through cell lysis.
What happens in the attachment phase during the multiplication of a T-even, lytic, double-stranded DNA, bacteriophage?
The phage attaches to the surface of the host cell.
What happens in the penetration phase during the multiplication of a T-even, lytic, double-stranded DNA, bacteriophage?
Enzymes allow the virus to digest part of the cell wall and the page injects its DNA into the cell.
What happens in the biosynthesis phase during the multiplication of a T-even, lytic, double-stranded DNA, bacteriophage?
- Viral DNA is used as a template to produce more viral components.
- The viral DNA is replicated through the host cell’s DNA replication process.
- Viral proteins are made through transcription and translation using the host cell’s components.
What happens in the maturation phase during the multiplication of a T-even, lytic, double-stranded DNA, bacteriophage?
Viral components self-assemble into virions.
What is a virion?
The complete, infective form of a virus outside a host cell, with a core of RNA or DNA and a capsid.
What is the complete, infective form of a virus outside a host cell, with a core of RNA or DNA and a capsid?
A virion
What happens during the release phase of a lytic, double-stranded DNA, T-even bacteriophage?
Viral lysozymes break down the cell well, lysing the cell and releasing new virions.
During what stage of a T-even, double-stranded DNA, lytic bacteriophage do viral lysozymes break down the cell well, lysing the cell and releasing new virions?
The release phase.
During what stage of a T-even, double-stranded DNA, lytic bacteriophage do viral components self-assemble into virions?
The maturation stage
During what stage of a T-even, double-stranded DNA, lytic bacteriophage is viral DNA used as a template to produce more viral components?
The biosynthesis phase
During what stage of a T-even, double-stranded DNA, lytic bacteriophage is viral DNA replicated through the host cell’s DNA replication process?
The biosynthesis phase
During what stage of a T-even, double-stranded DNA, lytic bacteriophage do the viral proteins get made through transcription and translation using the host cell’s components?
The biosynthesis phase
During what stage of a T-even, double-stranded DNA, lytic bacteriophage do enzymes allow the virus to digest part of the cell wall and the phage injects its DNA into the cell?
The penetration phase
During what stage of a T-even, double-stranded DNA, lytic bacteriophage does the phage attach to the surface of the host cell?
The attachment phase
During the lysogenic cycle, instead of killing the host, the phage genome integrates into the bacterial chromosome and becomes part of the host. What is the integrated phage genome called?
The prophase
What is the prophase in lysogenic viral cycle?
During the lysogenic cycle, instead of killing the host, the phage genome integrates into the bacterial chromosome and becomes part of the host. The integrated phage genome is called a prophage.
What is a lysogene?
A bacterial host with a prophage is called a lysogen.
What are the steps of the lysogenic cycle of the bacteriophage lambda?
- Attachment (Lytic cycle): The phage attaches to the surface of the host cell.
- Penetration (Lytic cycle): Enzymes allow the virus to digest part of the cell wall and the page injects its DNA into the cell.
- At this point, the liner phage DNA circularizes and could enter into the lysogenic cycle or continue through the lytic cycle.
- If the cell goes through they lysogenic cycle, the page DNA recombines with the bacterial chromosome. The integrated phage DNA is known as a prophage.
- Repressors prevent expression of most of the prophage genes, and the prophage is copied along with the rest of the chromosome when the cell reproduces, passing the prophage down to all of the decedent cells.
- The prophage can be excised from the chromosome and circularize. This occurs randomly at a low rate and happens more often in response to DNA damage. The phage can then reenter the lysogenic cycle or enter the lytic cycle.
- Biosynthesis (Lytic cycle): Viral DNA is used as a template to produce more viral components. The viral DNA is replicated through the host cell’s DNA replication process, viral proteins are made though transcription and translation using the host cell’s components.
- Maturation (Lytic cycle): Viral components self-assemble into virions.
- Release (Lytic cycle): Viral lysozyme breaks down the cell wall, lysing the cell and releasing new virions.
What is phage conversion?
Phage conversion is the alteration of host characteristics or phenotypes due to the presence of phage. This can include changes that prevent re-infection by the same phage or larger changes, such as Corynebacterium diphtheriae gaining the ability to express a new toxin.
What is the alteration of host characteristics or phenotypes due to the presence of phage called?
Phage conversion
What is specialized conduction?
Specialized transduction is transfer of a specific piece of bacterial chromosomal DNA near the site of integration by the phage. This piece of DNA can be transferred and expressed in a new host, but only when that new host has an integrated prophage.
What is the transfer of a specific piece of bacterial chromosomal DNA near the site of integration by the phage called?
Specialized transduction
What is lysogeny?
The type of life cycle that takes place when a bacteriophage infects certain types of bacteria.
The type of life cycle that takes place when a bacteriophage infects certain types of bacteria is called what?
Lysogeny
How does phage conversion explain why not all Corynebacterium diphtheriae cells are able to cause diphtheria?
C. diphtheriae can only produce the toxin when it carries the lysogenic phage. This is an example of phage conversion.
Describe the seven events in the multiplication of a DNA-containing virus, such as Papovavirus.
- Virion attaches to host cell.
- Virion enters cell and the viral DNA is uncoated.
- The viral DNA moves into the nucleus.
- A portion of the viral DNA is transcribed (the “early” genes)
- These are genes responsible for the replication of the viral DNA Viral DNA is replicated and some viral proteins are made.
- The “late” portion of the viral DNA is transcribed.
- This includes the capsid proteins and other viral proteins.
- The virions mature (assemble) within the cell.
- The virions are released from the host cell.
Where in the host cell does the genome of a Papovirus DNA virus go to allow the virus to replicate?
The DNA genome must move to the nucleus because DNA replication and transcription are required for replication.
Describe the difference between + strand single stranded RNA and - strand single stranded RNA.
The + strand is the “sense” strand. Proteins can be directly translated from the + strand.
The – strand is the “antisense” strand. The – strand is the cognate of the + strand. It is the RNA sequence that is able to bind to the + strand. The – strand cannot be translated. In order to make proteins, a virus with a – strand genome must first use the – strand as a template to make the + strand.
Describe the events of biosynthesis of animal viruses with + strand single stranded RNA genomes, - strand single stranded RNA genomes, and double stranded RNA genomes.
- Attachment, entry, and uncoating are similar to DNA animal viruses
- Biosynthesis varies depending on genome type
- strand viruses
1. After uncoating, the proteins can be directly translated from the + strand
2. The + strand is used as a template to make – strands
3. Strand viruses- The – strands are then used as a template to make more + strands, which can act as templates to produce more viral proteins or can act as viral genomes
- The – strand is used as a template to make + strands
- The + strands act as templates to produce more viral proteins or to produce more – strands to act as new viral genomes
- Double-stranded RNA viruses
- strands are produced inside the capsid and released into the cytoplasm of the host cell, which act as mRNA to make viral proteins
- RNA polymerase initiates production of – strands, which combine with the new + strands to make new viral genomes
- strand viruses
Where in the host cell does genome of a RNA virus go to allow the virus to replicate?
RNA viruses stay in the cytoplasm. They use their own enzyme (an RNA-dependent RNA polymerase) to copy their genomes and use the host cell’s ribosomes and tRNA to synthesize viral proteins. They do not need nuclear enzymes (i.e. enzymes and factors involved in DNA replication or transcription).
Describe the multiplication cycle of the HIV retrovirus.
- The retrovirus enters by fusion between attachment spikes and the host cell receptors.
- Uncoating releases the two single stranded RNA genomes and reverse transcriptase and integrase.
- The reverse transcriptase uses the viral genome RNA as a template to make a double-stranded molecule of DNA with the same sequence.
- The viral DNA moves into the nucleus and integrase combines it with the host cell DNA. The integrated viral DNA is referred to as a provirus.
- The provirus is used as a template for transcription, producing RNA copies of the provirus. These RNA copies can be used as:
- mRNA templates to make new viral proteins
- New viral genomes.
- The viral proteins assemble around two RNA copies of the provirus.
- The complex buds out of the host cell and becomes an infectious virion.
(Note that the provirus remains in the cell. Virions consist of proteins and RNA, which are produced by the provirus.)
Describe what an oncogenic virus is.
Oncogenic viruses are viruses that are able to cause tumors in animals. Some oncogenic viruses cause tumor formation because they possess oncogenes. Oncogenes are cellular genes that are involved in the cell cycle. Some oncogenic viruses have picked up oncogenes from their hosts and carry them to other cells, causing uncontrolled cell growth.
Viruses can also cause cancer by integrating their provirus in the host cell genome near genes involved in the cell cycle or near tumor suppressor genes. A nearby provirus can alter the levels that these proteins are produced at, thus causing cancer.
Describe what prions are and how they cause disease.
Prions are infectious proteins. The prion (PrP) protein has two confirmations, PrPC is the cellular form of the protein and PrPSc is the infectious form of the protein. The PrPSc form can convert PrPC to PrPSc. PrPSc builds up inside cells and leads to cell death. When the cell lyses, it releases all of the PrPSc, which then convert the PrPC of neighboring cells. This occurs in brain tissue which leads to lesions forming in the brain.
The switch to the PrPSc protein can be caused by infection of PrPSc from another source or can occur by PrP spontaneously miss folding into the PrPSc form. Some mutations in the PrP gene can make the spontaneous conversion more likely, which is the source of heritable prion diseases.
The prion (PrP) protein has what two confirmations?
PrPc (cellular form) and PrPSc (infectious form)
What are diseases caused by prions?
- Mad cow disease (cows)
- Creutzfeldt-Jakob syndrome
- kuru
- fatal fetal insomnia
- scrapie (sheep)
- chronic wasting disease (deer)
What are viroids?
Viroids are infectious RNA molecules. They do not encode proteins. They commonly infect plants and cause several diseases that can have economic impacts on agriculture.
On what industry do viroids have an economic impact?
Agriculture
What is an infectious RNA molecules that does not encode proteins and commonly infect plants and cause several diseases that can have economic impacts on agriculture.
A viroid
What are infectious proteins with two confirmations, one which builds up in cells and leads to death?
Prions
In prions, the PrPSc form can convert PrPC to what?
To PrPSc
What are two ways that PrPc switches to PrPSc?
The switch to the PrPSc protein can be caused by infection of PrPSc from another source or can occur by PrP spontaneously miss folding into the PrPSc form.
Is there such a thing as heritable prion diseases?
Yes. Some mutations in the PrP gene can make the spontaneous conversion more likely, which is the source of heritable prion diseases.
When PrPSc builds up inside cells and the cell lyses, it releases all of the PrPSc, which does what?
Converts the PrPC of neighboring cells.
What occurs in brain tissue which leads to lesions forming in the brain?
The PrPSc converts the surrounding PrPc.
Are prions RNA or DNA?
RNA
What is integrase?
Integrase is the viral enzyme that catalyzes the integration of virally derived DNA into the host cell DNA in the nucleus, forming a provirus.
How does the HIV retrovirus enter a cell?
The retrovirus enters by fusion between attachment spikes and the host cell receptors.
What happens during uncoating of the HIV retrovirus?
During uncoating of the HIV retrovirus, two single stranded RNA genomes and reverse transcriptase and integrase are released.
What purpose does reverse transcriptase serve in the multiplication of HIV retrovirus?
The reverse transcriptase uses the viral genome RNA as a template to make a double-stranded molecule of DNA with the same sequence.
What enzyme uses the viral genome RNA as a template to make a double-stranded molecule of DNA with the same sequence?
Reverse transcriptase
In HIV retrovirus multiplication, what moves into the nucleus?
The viral DNA moves into the nucleus and integrase combines it with the host cell DNA. The integrated viral DNA is referred to as a provirus.
What function does integrase serve in multiplication of the HIV retrovirus?
The viral DNA moves into the nucleus and integrase combines it with the host cell DNA.
The integrated viral DNA from the HIV retrovirus is referred to as a provirus which is used as a template for transcription, producing RNA copies of the provirus. These RNA copies can be used as what?
- mRNA templates to make new viral proteins
- New viral genomes
What happens in HIV retrovirus multiplication when the viral proteins assemble around two RNA copies of the provirus?
The complex buds out of the host cell and becomes an infectious virion.
(Note that the provirus remains in the cell. Virions consist of proteins and RNA, which are produced by the provirus.)
In what virus does the complex bud out of the host cell and become an infectious virion?
HIV retrovirus
In HIV retrovirus, virions consist of what two molecules and what produces them?
Molecules: Proteins and RNA
What produces them: The provirus
Complex viruses have more complicated structures that which three?
Than helical, polyhedral or enveloped viruses
What shape is the head of a bacteriophage?
Bacteriophages have a polyhedral head.
What does the head of a bacteriophage contain?
The head contains the viral nucleic acid.
Besides the polyhedral head which contains tehe viral nucleic acid, what other structures does it have?
It also has a helical tail sheath and other structures including a base plate and tail fibers.
What complex virus has a helical tail sheath and other structures including a base plate and tail fibers.
A bacteriophage
