Study sets, textbooks, questions
Upgrade to remove ads
BIOL 351 Test 2 (Old Stuff, 13-16)
Terms in this set (164)
What do ribosomes use as energy to move along mRNA?
Formation of peptide bonds is catalyzed by _______ rRNA.
For one master copy of DNA, you get multiple segments of _____. It would be good to have proofreading activity in transcription, but you won't "die" without it.
1- Codon Recognition
2- Peptide Bond Formation
3- Translocation, requires EF-Tu and EF-Ts
4. Cycle continues three times.
What are the 4 steps of transcription?
These are a complex formed by ribosomes that are simultaneously translating mRNA. (For RNA, there are multiple ribosomes and each ribosome makes protein products. mRNA has to be tightly regulated; you have to control transcription because different genes transcribe at different rates).
It becomes more and more stable through folding.
What occurs as far as folding patterns are concerned with a polypeptide?
Interactions of the R groups force the molecule to twist and fold in a certain way
Three-dimensional shape of polypeptide
Number and types of polypeptides that make a protein
Arrangement of subunits
What is a good example of quaternary structure?
What does Dr. Nan consider to be the most important aspect for proteins?
They take an improperly folded protein and either (1) properly fold it or (2) pass it on to molecule chaperones GroEL and GroES to properly fold it. Both of these processes require ATP.
What is the role of dnaK and dnaJ?
These are found on protiens requiring transport from the cell.
How many residues typically are signal sequences?
Found at the beginning of the protein molecule
Where are signal sequences found?
They prevent protein from completely folding.
What do signal sequences prevent?
The Sec system transports and secretes the unfolded proteins. These proteins possess a signal sequence that is recognizable by Sec A. This is either moved through the membrane to the periplasm, or is inserted into the membrane.
What is the role of the Sec system?
It only transports linear peptides across a membrane
What does the Sec System transport across a membrane?
They begin to fold - this folding is sometimes spontaneous or with the help of other proteins.
What occurs when the protein is outside?
It is the twin-arginine translocation system. It secretes folded proteins.
What is the Tat system?
Tat Protein Export System
Proteins that are folded in the cytoplasm are exported by this transport system that is distinct from the Sec system
It recognizes a signal sequence containing a pair of arginines.
What is unique about the signal sequence that Tat system recognizes?
For both Sec and Tat, signal peptides are removed once the protein has been...
There are types 1 through IX. They are all large complex of proteins that form channels through membranes.
How else are other proteins secreted through the membrane?
Types II and V
What systems are dependent on Sec or Tat?
Types I, III, IV, and VI
What are do not depend on or are require Sec or Tat?
Heritable change in DNA sequence that can lead to a change in PHENOTYPE
Observable properties of an organism
Mutation can lead to a change in ________.
A strain of any cell or virus differing from parental strain in genotype
This is the nucleotide sequence of genome.
This typically refers to strain isolated from nature
- Those that give the mutant a growth advantage under certain conditions or a distinguishable phenotype
- Useful in genetic research
- Those that usually have neither an advantage nor a disadvantage over the parent
- Detecting such mutations requires examining a large number of colonies and looking for differences (screening)
______ is always more tedious than selection.
What is the example of the method to facilitate screening called?
Replica plating is useful for identifying cells that have a nutritional requirement for growth.
What is replica plating useful for?
Cells with a nutritional requirement for growth
You take from a master plate, transfer colonies to a fresh medium that is either complete or selective, then the species are incubated and examined. On the complete medium, all grow. On the selective, the mutants do not grow.
How does replica plating work?
Those made environmentally or deliberately
- Can result from exposure to natural radiation or oxygen radicals
Those that occur without external intervention
This is one nucleotide change.
- These mutations change only one base pair
- They can lead to single amino acid change in a protein, an incomplete protein, or no change at all
- This codes for the same thing.
- Does not affect amino acid sequence
- Encodes a different protein sequence
- Amino acid changed; polypeptide altered
- New codon doesn't code for anything.
- Codon becomes stop codon; polypeptide is incomplete
Deletions or insertions that result in a shift in the reading frame
- Amino acids after mutation point become totally different.
- _______ mutations are usually lethal, or cause a large change.
- Can be -1, +1, when a normal protein is 0
Loss of Gene Function
What do frameshift mutations often result in?
Point mutations are typically _______.
_______: This is the alteration in DNA that reverses the effects of a prior mutation. (the second mutation reverses the other)
This is the strain in which the original phenotype is stored.
What are the two types of revertants?
This is when the mutation is at the same site as the original mutation.
This is when the mutation is at a different site in the DNA.
The mutation compensates for the effect of the original mutation.
10^-6 to 10^-7 per kilobase per gene
For most microorganisms, errors in DNA replication occur at what frequency?
This makes practical use of bacterial mutations to detect for potentially hazardous chemicals.
It looks for an increase in mutation of bacteria in the presence of a mutagen.
- A wide variety of chemicals have been screened for toxicity and carcinogenicity.
How does the Ames test work?
Increase the rate of reversion, which potentially shows a mutation.
- The mutation fro bacteria could be potentially carcinogenic for humans.
What does the chemical do in the Ames test?
These are chemical, physical, or biological agents that increase mutation rates.
Nucleotide Base Analogs
What are the classes of chemical mutagens?
Nucleotide base Analogs
These resemble nucleotides, directly incorporated into DNA, and introduce mutations during replication.
___ ________ induce chemical modifications.
Alkylating agent such as nitrosoguanidine
What is an example of a chemical mutagen?
These insert between base pairs and cause frameshift mutations.
What i san example of a intercalating agent?
What are the two main categories of mutagenic electromagnetic radiation?
This is UV radiation.
If you add ATT, ____ can link the two T's tighter and then the replicator cannot tell if it is one, two, or three T's making it a potential frameshift mutation.
Purines and pyrimidines
_____ and __________ strongly absorb UV.
What is one effect of UV radiation?
These are X-rays, cosmic rays, and gamma rays
They ionize water and produce free radicals.
What is the role of ionizing mutagenic electromagnetic radiation?
mutated base is still recognizable and can be repaired without referring to other strand
Repair of Single Stranded DNA
damaged DNA is removed and repaired using opposite strand as template
Repair of Double Strand Damage
a break in the DNA
- requires more error-prone repair mechanisms
Can induce bond consequences
No - it is counterproductive because it prevents evolution.
Is perfect fidelity in organisms productive or not?
Hyperaccurate or hypermutable
The mutation rate of an organism is subject to change. Mutants can be isolated from strains that are ________ or ________.
Hypermutable (Mutable) Strains
bacteria that benefit from increased mutation rates, such as dnaQ mutants (dnaQ encodes the proof-reading enzyme in DNA polymerase III )
SOS Regulatory System
What is the repair system that is used when DNA damage is large scale? (damage interferes with DNA replication,
The SOS Regulatory system is ____-________. It allows replication to proceed and cell to replicate, but errors are more likely.
DNA polymerases IV and V
What carries out the SOS regulatory system?
It allows for DNA to be synthesized with no template.
What does the SOS system allow?
The LexA protein is a transcription repressor of many genes, as shown in figure 11.9. In the green of the lower right corner, this is the feedback mechanism of LexA.
LexA has a negative feedback loop --> this negative feedback is indicative of biological system. In addition to this, LexA suppresses transcription of certain proteins. This can become a positive feedback circle as the product is increased, causing the suppression of LexA or vice versa depending on if it is positive or negative loop.
Describe how the SOS system works.
What are the three mechanisms of genetic exchange?
A cell accepts foreign DNA from environment
The gene transfer occurs using phage (bacterial virus) as a vector.
This is the mating (two different cell types mate with each other and exchange genetic information)
What are the three fates of horizontal gene transfer?
(this means the genetic change occurs between different cells, two different species, or replication that is done by us these are what we really care about in genetics)
What is horizontal gene transfer?
Most cells have a defense system; they do not accept foreign DNA
Transfer of a plasmid into the recipient cell (chromosomal element that replicate independently)
Physical exchange of DNA between genetic elements
- Have two pieces of DNA and they actually phase; change some fragment
Process that results in genetic exchange between homologous DNA from two different sources (Figure 11.11). RecA is essential
The two DNA pieces that participate in this are very similar. For example, if you have two pieces of DNA and the gene is argA (in which there is a point mutation that causes argA to be non-functional, causing it to be Arg-). If you have another piece of DNA reaching the argA gene, which is the in tact functional DNA?
You put these both into the same cell and at a very low frequency, the two pieces are changed and the functional argA DNA will replace the non-functional argA DNA which fixes the "bubble." We call this homologous recombincation because the two pieces are very similar except for one point mutation.
Describe Homologous Recombination
We select for this by using a plate which doesn't contain arginine.
How do we select for this?
What kind of medium is used to detect rare genetic recombinants?
1. Endonuclease nicks the donor DNA.
2. The SSB protein binds.
3. The recipient strand is invaded by RecA protein.
4. There is development of a cross-strand exchange.
5. Resolution occurs at specific sites, leading to patches (non-crossover) and splices (crossovers)
What is the 5 step process of homologous recombination?
Holliday Intermediate (Heteroduplex)
What is the cross-strand exchange that is developed called?
Cutting of the holliday intermediate in 1 and 2
How does a patch result?
Cutting of holliday intermediate in 3 and 4
How does a splice occur?
Genetic transfer process by which DNA is incorporated into a recipient cell and brings about genetic change (this DNA transfer will cause a phenotype)
cells are capable of taking up DNA and being transformed
Many ______ bacterial are naturally competent.
In naturally transformable bacteria, _______ is regulated. In other strains, specific procedures are necessary to make cells competent.
Chemicals, such as Ca2+
What can "turn cells competent?"
What can be used to force cells to take up DNA? What is this more specifically called?
1. DNA binds (transforming DNA from donor cell).
2. Uptake of single-stranded DNA
3. RecA mediated homologous recombination.
4. The cell is transformed.
Describe the natural transformation of G+ bacteria by single strand DNA.
Transfer of DNA from one cell to another by a bacteriophage
What are the two modes of transduction?
DNA derived from virtually any portion of the host genome is packaged inside the mature virion (Figure 11.15)
Defective virus particle incorporates fragment of the cell's chromosome randomly
DNA from a specific region of the host chromosome is integrated directly in the virus genome
- DNA of temperate virus excises incorrectly and takes adjacent host genes along with it
- Transducing efficiency can be high
alteration of the phenotype of a host cell by a lysogenization (phage DNA incorporates into bacterial chromosome and becomes dormant)
It becomes immune to further infection by the same phage.
What occurs in the host cell after phage conversion?
Nondefective temperate phage _______ a cell and becomes a prophage.
Other phenotypic changes can also occur
- Salmonella enterica serovar
- Anatum and bacteriophage ε
Corynebacterium diphtheriae and bacteriophage β
What other phenotypic changes can occur in phage conversion?
Bacterial Conjugation (Mating)
mechanism of genetic transfer that involves cell-to-cell contact
Bacterial conjugation is a _______ encoded mechanism.
contains conjugative plasmid (F+)
does not contain plasmid (F-)
F (fertility) Plasmid
- Circular DNA molecule; ~100 kbp
-Contains genes that regulate DNA replication
-Contains several transposable elements that allow the plasmid to integrate into the host chromosome
-Contains tra genes that encode transfer functions
These are within the fertility plasmid and they encode transfer functions.
What are tra genes?
What is necessary for DNA transfer by conjugation?
Rolling Circle Replication
How is DNA synthesized in this case?
- The F plasmid has two origins: oriV - meaning it is the origin we commonly talk about, it starts here) and oriT (transfer origin, meaning that
DNA transfer starts from here).
- DNA transfer has to have a region site because during conjugation the DNA is newly synthesized using a rolling circle mechanism.
The picture above is a F+ and F- cell; the f+ willl most likely have type 4 pili.
Describe the Rolling circle replication.
Piilus with attached ______ ______ is used for conjugation.
Transfer of Plasmid DNA by conjugation
1. The pilus retracts.
2. Cell Pairs are stabilized and the F plasmid is nicked in one strand.
3. Transfer of one strand from F+ to F= cell. F plasmid simultaneously replicated in F+ cell.
4. Synthesis of the complementary strand beings in the recipient strand.
5. Completion of DNA transfer and synthesis - These cells separate.
What are cells called that possess a nonintegrated F plasmid?
Cells possessing an integrated F plasmid are called ______.
High Frequency of Recombination
What does Hfr stand for?
High rates of genetic recombination between genes on the donor chromosome and those of the recipient
What does Hfr mean?
- Ability to synthesize F pilus
- Mobilization of DNA for transfer to another cell
- **Alteration of surface receptors so that cell can no longer act as a recipient in conjugation
The presence of the F plasmid results in alterations in cell properties. What are some common examples of this?
These are mobile elements. These are present in both the F plasmid and E. coli chromosome, which facilitate homologous recombination
The plasmid is now apart of the chromosome. The chromosomal genes are transferred with plasmid.
At this point, where is the plasmid?
Recipient cell remains as F- and does not become Hfr because only a portion of the integrated F plasmid is transferred by the donor
What occurs within the recipient cell?
Discrete segments of DNA that move as a unit from one location to another within other DNA molecules are
All 3 domains of life
Where are transposable elements found?
What is the process of movement for transposable elements?
Frequency of transposition is 1 in 1000 to 1 in 10,000,000 per generation
First observed by Barbara McClintock
What is the frequency of transposition? Who observed this?
What are two main types of transposable elements in bacteria?
These both carry genes encoding __________.
These both have _____ _____ at their ends.
______ _______ are the simplest transposable element
~1000 nucleotides long
Inverted repeats are 10-50 base pairs
Only gene is for the transposase
Found in plasmids and chromosomes of Bacteria and Archaea
Found in some bacteriophages
________ are larger than insertion sequences
- Transposase moves any DNA between inverted repeats
- Insertion of a transposable element generates a duplicate target sequence (Figure 11.29)
- May include antibiotic resistance
Examples are Tn5 (kanr) and Tn10 (tetr)
__________ moves any DNA between inverted repeats
What are the mechanisms of transposition?
transposon is excised from one location and reinserted at a second location (e.g., Tn5; Figure 11.30)
- Number of transposons stays constant
- The donor DNA will just cut the transposon out and send the information to the recipient. This mechanism does not make much sense.
a new copy of transposon is produced and inserted at a second location
- Number of transposons present doubles
- This mechanism makes much more sense.
Transposons with antibiotic resistance are used
How do we use transposons to make mutants?
In this case, the transposon is on a plasmid that cannot be ______ in the cell. The cells capable of growing on selective medium likely acquired transposon. Most of these insertions will be in genes that encode proteins.
Screen for the loss of function to determine the insertion site
What is the nex step?
Clustered Regulatory Interspaced Short Palindromic Repeats
Prokaryotic Immune System
- First discovered in bacteria, serves as a bacterial immune system, relies on the Cas protein
- Region of bacterial chromosome containing DNA sequences similar to foreign DNA (spacers) alternating with identical repeated sequences
region of bacterial chromosome containing DNA sequences similar to foreign DNA (________)
What are CRISPR-associated proteins?
Obtain and store segments of foreign DNA as spacers
Recognize and destroy foreign DNA
What are the roles of CAs proteins?
Cas proteins of CRISPR systems function as endonucleases when guided to nucleic acids.
Synthetic RNA (synthetic guide RNA [sgRNA]) that recruits Streptococcus Cas9 and binds to target DNA enables cutting in genome of almost any cell; DNA can be ligated or used to insert new DNA. (Figure 12.36)
Cutting requires protospacer adjacent motif (PAM, 3 bp)
Homologous recombination can be used to incorporate new DNA.
Nonhomologous double-stranded DNA break repair pathway can ligate after deletion.
How does sequence targeting by the Cas9 protein work?
Synthetic guide RNA (sgRNA)
________ _________ that recruits Streptococcus Cas9 and binds to target DNA enables cutting in genome of almost any cell; DNA can be ligated or used to insert new DNA.
Cutting requires protospacer adjacent _______ (________, 3 bp)
Spacer Sequence (light green in figure 10.28)
What is the important sequence?
Cas-introduced double strand breaks provide opportunities for ____ _____.
The largest piece of information
In this case, cut the DNA from two different locations and fuse the rest of the DNA out --> what does this form?
Make a deletion, cut open sequence in the middle, make an insertion, make a large deletion or rearrangement
- We can use this system to regulation transcription of a gene
What are applications of CRISPR-Cas9?
Recommended textbook explanations
Human Physiology: From Cells to Systems
Human Physiology: From Cells to Systems
Molecular Biology of the Cell
Alexander Johnson, Bruce Alberts, Julian Lewis
Kenneth R. Miller, Levine
Sets with similar terms
Gene transfer, Mutations, and Genome evolution (Ch…
Microbiology: Bacterial Genetics. CH. 8
Micro Ch. 6
Microbiology Chapters 13+14 Mutants and Mutations
Other sets by this creator
CHES AREA VII: Promote, and Advocate for Health, H…
CHES AREA VI: Serve as a Health Education/Promotio…
CHES AREA V: Administer and Manage Health Educatio…