Chapters #11 & #12 Flashcards
(77 cards)
1
Q
Similarities between Prokaryotes and Eukaryotes
A
-plasma membrane
-DNA
-cytoplasm
-ribosomes
2
Q
What do Eukaryotes have that Prokaryotes do not
A
-nucleus
-nuclear membrane
3
Q
Classes of Mutations
A
- Point mutation/base substitution
- Insertion/Deletion
- Inversion
4
Q
Point Mutation/Base substitution
A
when a single nucleotide is changed in a DNA sequence
-Silent mutation
-Missense Mutation
-Nonsense mutation
5
Q
Silent Mutation
A
a mutation that has no effect on the protein sequence
6
Q
Missense Mutation
A
results in an amino acid substitution
7
Q
Nonsense mutation
A
substitutes a stop codon for an amino acid
8
Q
Insertion/Deletion
A
involves the addition or subtraction of one or more nucleotides; results in a shift in the reading frame
9
Q
frameshift mutation
A
he insertion or deletion of nucleotide bases in numbers that are not multiples of three. This is important because a cell reads a gene’s code in groups of three bases when making a protein
10
Q
Inversion
A
occurs when a fragment of DNA is flipped
in orientation in relation to the DNA on the other side
11
Q
What causes mutations?
A
-a “mistake” by DNA polymerase that fails to be repaired
-physical agents
-chemical agents
12
Q
examples of physical agents that cause mutations
A
-cosmic rays
-X-rays
-UV radiation – cause pyrimidine dimers
13
Q
examples of chemical agents that cause mutations
A
-reactive oxygen molecules (H2O2)
-superoxide radicals (*O2–)
-acridine orange (intercalating agent)
-certain biological processes (mutator strains)
14
Q
oxidation of nucleotides makes a mutagen
A
-Adenosine nucleoside normally base-pairs by hydrogen bonds with an oxygen and a hydrogen of a thymine or uracil nucleotide
-Altered adenine will hydrogen bond with a hydrogen and a nitrogen of a cytosine nucleotide
-The altered adenine pairs with cytosine instead of thymine
15
Q
Types of DNA repair
A
-Base excision repair
-methyl mismatch repair
-SOS (‘save our ship’) repair
-DNA recombination
16
Q
Base excision repair
A
Recognizes a specific damaged base and removes it from the DNA backbone
17
Q
Methyl mismatch repair
A
Requires recognition of the methylation pattern in DNA bases
18
Q
SOS (‘save our ship’) repair
A
Coordinated cellular response to damage that can introduce mutations in order to save the cell
19
Q
DNA recombination
A
The process of “crossing over” and exchange of
two DNA helices
20
Q
Levels of gene regulation
A
-changing the DNA sequence
-control of transcription
-translational control
-post-translational control
21
Q
Changing the DNA sequence
A
Some microbes change the DNA sequence to activate or disable a particular gene. Ex: phase variation
22
Q
Control of transcription
A
Transcription can be regulated by protein repressors, activators, and alternative sigma factors
23
Q
Translational control
A
Control of transcription initiation sequences that recognize specific repressor proteins
24
Q
Post-translational control
A
Control of proteins that are already made
25
ionizing radiation
-like X-rays and gamma rays can cause single- and double-stranded breaks in the DNA backbone through the formation of hydroxyl radicals on radiation exposure
-Ionizing radiation can also modify bases; for example, the deamination of cytosine to uracil, analogous to the action of nitrous acid
26
non-ionizing radiation
-can induce dimer formation between two adjacent pyrimidine bases, commonly two thymines, within a nucleotide strand
-During thymine dimer formation, the two adjacent thymines become covalently linked and, if left unrepaired, both DNA replication and transcription are stalled at this point
-DNA polymerase may proceed and replicate the dimer incorrectly, potentially leading to frameshift or point mutations
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nucleotide excision repair
(also called dark repair), enzymes remove the pyrimidine dimer and replace it with the correct nucleotides
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Photoreactivation
-(in the presence of light) An enzyme called photolyase recognizes the distortion in the DNA helix caused by the thymine dimer and binds to the dimer
-Then, in the presence of visible light, the photolyase enzyme changes conformation and breaks apart the thymine dimer, allowing the thymines to again correctly base pair with the adenines on the complementary strand
29
Operon
In bacteria and archaea, structural proteins with related functions are usually encoded together within the genome in a block called an operon and are transcribed together under the control of a single promoter, resulting in the formation of a polycistronic transcript
30
Repressor
a transcription factor that suppresses transcription of a gene in response to an external stimulus by binding to a DNA sequence within the regulatory region called the operator
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Operator
located between the RNA polymerase binding site of the promoter and the transcriptional start site of the first structural gene
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Induction
begins the transcriptional and translational activities
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Repression
stops the transcriptional and translational activities
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How do cells assign tasks to respond to changes inside the cell or respond to outside influences?
1. Sensing the intracellular environment
2. Global regulators
3. Sensing the extracellular environment
35
Sensing the intracellular environment
Different regulatory proteins bind to specific compounds to determine the compound’s concentration
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Global regulators
-Proteins that affect the expression of many
different genes are called global regulators.
-EX: cAMP receptor protein (CRP) of E. coli
and related species
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Sensing the extracellular environment
-A common mechanism used by bacteria to
sense outside of the cell and transmit that
information inside relies on a series of two-component protein phosphorylation relay
systems.
-Ex: Sensor kinase PhoQ in Salmonella
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Genetic Recombination
-Exchange of genes between two DNA molecules (Crossing over occurs when two chromosomes break and rejoin)
-vertical gene transfer
-horizontal gene transfer
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Vertical gene transfer
occurs during reproduction between generations of cells
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Horizontal gene transfer
-the transfer of genes between cells of the same generation
-Also called lateral gene transfer - transformation, transduction and conjugation
-Once the genetic information is transferred from the donor, it can enter the genome of the recipient by recombination
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Plasmids
-Mostly circular, double-stranded, extrachromosomal DNA
-Self-replicating by the same mechanisms as any other DNA
-Most of plasmids have been identified due to having some function they allow the bacterium to survive
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Plasmid functions
1. F plasmids direct synthesis of protein towards the pili
2. Resistance (R) plasmids carry genes that provide resistance to antimicrobials (chloramphenicol, arsenic, etc)
3. Virulence plasmids (neurotoxin) cause disease signs and symptoms
4. Tumor inducing plasmids – cause tumor formation in plants
5. Genes for catabolic enzymes – not essential for cell growth
6. Bacteriocinogen plasmid - Direct synthesis of
bacteriocins (bacteria killing)
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transposable elements or transposons
-Genes that can move from one chromosome to
another
-They exist in virtually all life forms
-Unlike plasmids, transposable elements cannot
replicate outside a larger DNA molecule
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transposase
All transposable elements include a transposase gene whose enzyme product moves the element from one DNA molecule into another
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A typical transposon encodes
the enzyme transposase surrounded by inverted repeat sequences
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Transposase facilitates
-recombination between inverted repeats and transposon is cut from its original location inserted into a new location
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Transformation
Importing free DNA from the environment into
bacterial cells
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Transformasome
-Natural transformation is a property inherent to many bacterial species and is carried out by specific protein complexes
-Streptococcus, Bacillus, Haemophilus, Neisseria = naturally competent
-E. coli, Salmonella = can be manipulated to be
made artificially competent
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Electroporation
A brief electrical pulse “shoots” DNA across the membrane
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The process of transformation
1. Competence factor (CF) is synthesized and exported
2. As cell numbers rise, external CF level increases and activates sensor kinase
3. The sensor kinase transfers a signal (phosphate) to a transcriptional activator that stimulates transcription of the transformasome genes
4. Transformasome binds extracellular DNA - one strand is transported; one strand is degraded
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Transduction
-Gene transfer is mediated by a bacteriophage (bacterial virus) vector
-Trans = across; ductio = to pull
-Originally discovered in Salmonella by Joshua Lederberg in 1952
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Bacteriophage
composed of core nucleic acid covered by a protein coat
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Specialized transduction
-occurs at the end of the lysogenic cycle, when the prophage is excised and the bacteriophage enters the lytic cycle
-Since the phage is integrated into the host genome, the prophage can replicate as part of the host
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Why is transduction significant?
1. Transfer genetic material from one bacterial cell to another and alters the genetic characteristics of the recipient cell
2. Incorporation of phage DNA into a bacterial chromosome demonstrates a close evolutionary relationship between the prophage and the host bacterial cell
3. The fact that a prophage can remain for long periods of time in a cell suggests a similar mechanism for the viral origin of cancer
4. The viruses bring along genes from their previous host (or hosts) thus, if this type of virus infects us, the type of DNA incorporated into us might belong to another animal AKA we might consider ourselves transgenic
5. It provides a way to study gene linkage to do chromosome mapping
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Conjugation
-Gene transfer requires contact between donor and recipient cells
-Larger quantities of DNA are transferred compared to Transduction or Transformation
-Originally discovered by Joshua Lederberg in 1946
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Typical Conjugation
1. Pilus of donor cell attaches to recipient cell. Pilus contracts, drawing cells together to make contact with one another
2. One strand of F plasmid DNA transfers from donor cell to recipient cell
3. Donor synthesizes complementary strand to restore plasmid. Recipient synthesizes complementary strand to become F+ cell with pilus
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Hfr cells
-the F plasmid occasionally integrates into the bacterial chromosome through recombination between the plasmid and the chromosome, forming an Hfr cell
-“Hfr” refers to the high frequency of recombination seen when recipient F− cells receive genetic information from Hfr cells through conjugation
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Why is conjugation significant?
1. Contributes to genetic variation
2. Increases genetic diversity (comparing to other mechanisms) - larger amounts of DNA are transferred
3. May represent an evolutionary stage between asexual processes and the actual fusion of whole cells (the gametes)
4. Plasmids are self-transmissible and can sometimes be promiscuous
5. Some Gram + bacteria have self-mating plasmids that do not form a F pili, instead they secrete peptide compounds which simulate nearby bacteria that do contain the plasmid to mate with them
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Plasmids in Biotechnology
-DNA plasmids have certain DNA sequences that can be cut by a specific enzyme called a restriction endonuclease
-Usually the restriction sequence is a “palindrome,” in which the sequence of base pairs reads the same forward and back
60
Restriction Enzymes
bacterial enzymes produced as a protection mechanism to cut and destroy foreign cytoplasmic DNA that is most commonly a result of bacteriophage infection
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Gel Electrophoresis
a technique commonly used to separate biological molecules based on size and biochemical characteristics, such as charge and polarity
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DNA Electrophoresis Steps
1. DNA sample loading
2. Application of electrical field (DC)
3. DNA separation
4. UV transillumination and documentation
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DNA Recombination
-a process by which pieces of DNA are broken and recombined to produce new combinations of alleles
-This recombination process creates genetic diversity at the level of genes that reflects differences in the DNA sequences of different organisms
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Gene Fusion
-Transposition of genes from one location of the chromosome to another - fusion of two genes together
-Depending on the design - a function may be inactivated or a function may be placed under the control of a different
regulatory sequence
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Protein Synthesis Machinery
-ribosomes (rRNA & proteins)
-transfer RNAs (tRNA)
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tRNA
-exist in the cytoplasm
-60 to 90 types
-Bind to specific codon on the mRNA template and add the specific amino acid to the polypeptide chain
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RNA transcription
the information encoded within the DNA sequence of one or more genes is transcribed into a strand of RNA
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Protein Synthesis (translation)
the second part of gene expression, involves the decoding by a ribosome of an mRNA message into a polypeptide product
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Steps of translation
1. Initiation
2. Elongation
3. Termination
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Initiation
translational complex forms, and tRNA brings first amino acid in polypeptide chain to bind to start codon on mRNA
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Elongation
tRNAs bring amino acids one by one to add to polypeptide chain
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Termination
release factor recognizes stop codon, translational complex dissociates, and completed polypeptide is released
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How do DNA molecules exchange genetic information?
DNA molecules exchange portions by breaking and re-forming their sugar-phosphate backbones
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Flow of Genetic Information Steps
1. Expression
2. Recombination
3. Replication
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Expression
Genetic information is used within a cell to produce the proteins needed for the cell to function (cell metabolizes & grows)
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Recombination
Genetic information can be transferred between cells of the same generation (recombinant cell)
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Replication
Genetic information can be transferred between generations of cells (daughter cells)
