Chapter 7 Flashcards
Gregor Mendel
Czech Austrian monk
Determined that traits are inherited as physical units now called genes.
George Beadle and Edward Tatum
Published a paper reporting that genes direct the production of enzymes
What common bread mold did Beadle and Tatum study?
Common bread molds. Neurospora species
What does DNA stand for
Deoxyribonucleic acid
What encodes a specific amino acid
A set of three nucleotides encodes a specific amino acid
DNA definition
DNA is the blueprint providing instructions for building an organisms components.
Structure of DNA
DNA itself is a simple structure.
A long linear or circular molecule composed of only four nucleotides, each containing a particular nucleobase: A,T,C,G.
Nucleotides
The subunit of nucleic acids
Nucleobase
The purine or pyramidine ring structure found in nucleotides; also called a base.
What does a string of amino acids make up
A string of amino acids make up a protein
What is the structure and function of proteins is dictated by:
The structure and function of proteins is dictated by the order of the amino acid subunits.
Genome
The complete set of genetic information of a cell or virus
The genome of all cells is composed of:
The genome of all cells is composed of DNA, but some viruses have an RNA genome.
Gene
The functional unit of the genome;
A gene encodes a product
What does a gene encode
A gene encodes a product.
Called the gene product, most commonly a protein.
Genomic
The study and analysis of the nucleotide sequence of DNA.
Study and analysis of genomes
All cells must accomplish two general tasks in order to multiply:
- The double stranded DNA must be duplicated before cell division so that it’s encoded information can be passed to the next generation (DNA replication.
- The information encoded by the DNA must be decoded so that the cell can synthesize the necessary gene products (Gene expression).
DNA replication
Duplication of a DNA molecule
Gene expression involves what two related events:
- Transcription
- Translation
Gene expression
Transcribing and then translating the information in DNA to produce the encoded protein.
Transcription
Is the process by which the information encoded in DNA is copied into a slightly different molecule: RNA.
Translation
The information carried by the RNA is interpreted and used to synthesize the encoded protein.
During translation, information encoded by mRNA transcript is used to synthesize a protein.
Central dogma of molecular biology
The flow of information from DNA—> RNA —> protein.
In-depth description of DNA structure:
DNA is usually double stranded, helical structure.
Each strand is a chain of deoxyribonucleotide subunits called nucleotides.
Each nucleotide consists of a 5 carbon sugar, a phosphate group, and one of four different nucleobase (ATGC).
What is each nucleotide in a DNA strand consist of
- 5-carbon sugar
- A phosphate group
- One of four different nucleobase (ATGC).
What is each nucleotide in a DNA strand consist of
- 5-carbon sugar (deoxyribose)
- A phosphate group
- One of four different nucleobase (ATGC).
How is the phosphate group attached to the 5’ carbon in a nucleotide
In a nucleotide, the phosphate group is attached to the 5’ carbon and is therefore referred to as the 5’PO4 (5 prime phosphate).
How are the nucleotides in a DNA molecule joined together?
The nucleotides of a DNA molecule are joined together by a covalent bond between the 5’PO4 (5 prime phosphate) of one nucleotide and the 3’OH (3 prime hydroxyl) of the next.
Joining the 5 prime phosphate of one nucleotide and the 3 prime hydroxyl of the next creates
a series of alternating sugar and phosphate units, called the sugar-phosphate backbone.
5’ end
The end of a nucleotide strand that has a phosphate group attached to the number 5 carbon of the sugar.
3’end
The end of a nucleotide strand that has a hydroxyl group attached to the number 3 carbon of the sugar.
How are the two strands of DNA held together?
The two strands of DNA are complementary, and are held together by hydrogen bonds between the nucleobases.
Adenine attaches to:
Thymine.
A-T bases are held together by two hydrogen bonds.
A-T bases are held together how
A-T bases are held together by two hydrogens bonds
Guanine attaches to:
Cytosine
These G-C bases are held together by three hydrogen bonds
C-G bases are held together by what
C-G bases are held together by three hydrogen bonds, a slightly stronger attraction than that of A-T pair.
Base pairing
The hydrogen bonding of A to T and G to C. It is a fundamental characteristic of DNA.
Because of the rules of base pairing….
One of the strands can always be used as a template for the synthesis of the opposing strand.
Antiparallel
Describes the opposing orientations of the two strands of DNA in a double helix.
The two strands are oriented in opposite directions.
How is each strand of DNA oriented?
One strand is oriented in the 5’ to 3’ direction, and it’s complement is oriented in the 3’ to 5’ direction.
Why are DNA strands generally quite stable
DNA is generally quite stable because of the numerous hydrogen bonds holding the strands together.
“Melting” or “Denaturing” DNA
Separating two strands is called melting of denaturing
Three differences between RNA and DNA
- The sugar in the nucleotides of RNA is ribose, not deoxyribose; it has an oxygen atom that deoxyribose does not.
- RNA contains the nucleobase uracil in place of the thymine found in DNA.
- RNA is usually a single stranded linear molecule much shorter than DNA.
How is RNA synthesized
RNA is synthesized using a region of one of the two strands of DNA as a template.
Is called transcript
What are the base pairing rules for RNA.
The base pairing rules apply except that uracil pairs with adenine.
What are the three different functional types of RNA required for gene expression and are transcribed from different sets of genes
- Messenger RNA (mRNA)
- Ribosomal RNA (rRNA)
- Transfer RNA (tRNA)
Most genes encode proteins and are transcribed into
mRNA
mRNA
Type of RNA molecule translated during protein synthesis
Which two types of RNA are never translated into proteins
- Ribosomal RNA (rRNA)
- Transfer RNA (tRNA)
Ribosomal RNA
Type of RNA molecule present in ribosomes
Transfer RNA
Type of RNA
molecule involved in interpreting the genetic code; each tRNA molecule carries a specific amino acid
Why do cells require mechanisms to regulate the expression of certain genes
Because although a cells DNA can encode thousands of different proteins, not all of them are needed at the same time or equal quantities.
What is a fundamental aspect of regulation of certain genes
A fundamental aspect of the regulation is the cells ability to quickly destroy mRNA.
How are mRNA destroyed in the cell; what does this provide the cell with
Transcripts are destroyed by cellular enzymes
Provides the cells with a means to control gene expression
How can a cell quickly change the levels of protein production
By simply regulating the synthesis of mRNA molecules.
Why is DNA replicated?
DNA is replicated so that each of the two cells generated during binary fission can receive one complete copy of the genome.
What direct does the replication process occur?
The replication process is generally bidirectional, meaning it proceeds in both directions.
Origin of replication
Distinct region of a DNA molecule at which replication is initiated.
Specific starting point of DNA replication.
Why is it better for replication to occur bidirectional than unidirectional?
This allows a chromosome to be replicated in half the time it would take if the process were unidirectional.
Replication fork
In DNA synthesis, the site at which the double helix is being unwound to expose the single strands that can function as templates for DNA synthesis.
Where do the replication forks ultimately meet when the process is complete?
The replication forks ultimately meet at a terminating site when the process is complete.
What do each of the two DNA molecules created through replication contain:
Each of the two DNA molecules created through replication contain one of the original strands paired with a newly synthesized strand.
What does it mean to say replication is ‘semi conservative’
Because one strand of the original molecule is conserved in new each molecule, replication is said to be semi conservative.
The process that starts DNA replication is called…
Initiation
When does initiation begin (replication)
This begins when specific proteins recognize and bind to the origin of replication ( a certain DNA sequence).
How many origin of replication do bacterial chromosome and plasmids have
Bacterial chromosomes and plasmids typically contain only one origin of replication, and a DNA molecule that lacks the sequence will not be replicated.
What proteins bind to the bacterial origin of replication
- DNA gyrase
- Helicases
DNA gyrases
Enzyme that helps relieve the tension in DNA caused by the unwinding of the two strands of DNA helix during DNA replication.
How does DNA gyrase work
The enzyme temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix.
Helicases
Enzyme that unwinds the DNA near the replication fork.
Primase
Enzyme that synthesizes small fragments of RNA to serve as primers for DNA synthesis during DNA replication.
They synthesize short stretches of RNA complementary to the exposed templates.
Primer
During DNA replication, an RNA molecule that initiates the synthesis of DNA; also a short DNA molecule used to initiate DNA synthesis in vitro.
Three differences between eukaryotic cells initiation processes and those of bacteria:
- Eukaryotic chromosomes typically have multiple origins of replication.
- The proteins involved in the replication process are different.
- DNA replication machinery of archaea are also distinct.
What happens once replication is initiated
Once replication is initiated, enzymes called dna polymerase synthesize DNA in the 5’ to 3’ direction, using one parent strand as a template to make the complement.
DNA polymerase
Enzyme that synthesizes DNA, using an existing strand as a template to make a new complementary strand.
What direction does DNA polymerase synthesize DNA
In the 5’ to 3’ direction.
What circumstances do DNA polymerase work
DNA polymerase add nucleotides only onto an existing nucleotide strand, so they cannot initiate synthesis.
Why is RNA primers required at the origin of replication
They provide the DNA polymerase with a molecule to which it can add additional nucleotides.
Replisome
A complex of enzymes and other proteins that cells use to replicate DNA
They simultaneously synthesize both strands at a replication fork.
How are additional template sequences revealed?
In order for replication to progress, the helicases must progressively unzip the DNA strands at each replication fork to reveal additional template sequences.
Leading strand
In DNA replication, the DNA strand that is synthesized as a continuous fragment.
Lagging strand
Is more complicated than synthesis of leading strands
In DNA replication, the strand that is synthesized as a series of fragments.
Why is synthesis of lagging strand more complicated than leading strand?
This is because DNA polymerase cannot add nucleotides to the 5’ end of a nucleotide chain, so synthesis must be reinitiated as additional template is exposed.
Each time synthesis is reinitiated, another RNA primer must be made first.
Each time DNA replication is initiated, what must be made and what results?
Each time synthesis is reinitiated, another RNA primer must be made first.
The result is a series of small fragments, each of which has a short stretch of RNA at its 5’ end. (Okazaki fragments)
Okazaki fragments
Nucleic acid fragment synthesized as a result of the discontinuous replication of the lagging strand of DNA.
As DNA polymerase add nucleotides to the 3’ end of one Okazaki fragment what happens?
As DNA polymerase adds nucleotides to the 3’ end of one Okazaki fragment, it eventually reaches the 5’ end of another.
A different type of DNA polymerase then removes the RNA primer nucleotides and simultaneously replaces them with deoxynucleotides.
DNA Ligase
Enzyme that forms covalent bonds between adjacent fragments of DNA.
An enzyme that seals the gaps between fragments by forming a covalent bond between the adjacent nucleotides.
How long does it take E.coli chromosome to be replicated
It’s takes approximately 40 minutes.
Why does it take Ecoli 40 minutes for its chromosome to be replicated but only have a generation time of 20 minutes
This happens because under favorable growing conditions, a cell can initiate a new round of replication before the preceding one is complete.
Polypeptide
A chain of amino acids
Protein
A functional molecule made up of one or more polypeptides.
What occurs during transcription
The enzyme RNA polymerase synthesizes single stranded RNA using DNA as a template
RNA polymerase
Enzyme that synthesizes RNA using one strand of DNA as a template.
How do the RNA polymerase know where to start and stop for transcription
Specific nucleotide sequences in DNA direct the polymerase where to start and stop for transcription.
Promotor
Nucleotide sequence to which RNA polymerase binds to start transcription
Terminator
In transcription, a DNA sequence that stops the process.
How is RNA polymerase similar to DNA polymerase
Like DNA polymerases, RNA polymerase can add nucleotides only to the 3’end of a chain, and therefore it synthesizes RNA in the 5’to 3’ direction.
How is DNA polymerase and RNA polymerase different?
Unlike DNA polymerases, RNA polymerase can start synthesis without primer.
The RNA made during transcription is ______ and ______ to the DNA strand that served as template
Complementary and antiparallel
Minus strand
The DNA strand used as a template for RNA synthesis
The complement to the plus (or sense) strand of RNA
What is another name for the minus (-) strand
Negative strand
Antisense strand
Plus (+) strand
The DNA strand complementary to the strand used as a template for RNA synthesis
An mRNA molecule that can be translated to make a protein.
Another name for plus (+) strand
Positive strand
Sense strand
Since the RNA is complementary to the (-) DNA strand
It’s Nucleotide sequence is the same as the (+) DNA strand, except that it contains uracil rather than thymine.
In prokaryotes, mRNA transcripts can be carried in two ways:
- Monocistronic
- Polycistronic
Cistron
Synonymous with a gene
Monocistronic
An RNA transcript that carries one gene
Polycistronic
Describes the mRNA molecule that carries the information for more than one gene.
The proteins encoded on a polycistronic message generally have related functions, allowing a cell to express related genes as one unit.
How does transcription begin
Transcription is initiated when RNA polymerase binds to a promotor
What happens when RNA polymerase binds to a promotor
The binding denatures (melts) a short stretch of DNA, creating a region of exposed nucleotides that serves as a template for RNA synthesis.
Sigma factor
Component of RNA polymerase that recognizes and binds to promoters.
Cells can produce various types of sigma factors, each recognizing different promoters.
What proteins do eukaryotic cells and archaea use to recognize promoters.
The RNA polymerases of eukaryotic cells and archaea use proteins called transcription factors to recognize promoters.
What else does a promoter do during transcription with a RNA polymerase
A promoter orients the direction of RNA polymerase on the DNA molecule
What dictates the direction of transcription and thereby determines which strand will be used as a template?
In identifying a region at which transcription begins, a promoter orients the direction of RNA polymerase on the DNA molecule.
In turn, this dictates the direction of transcription and thereby determines which strand will be used as a template.
Elongation phase
In the elongation phase, RNA polymerase moves along DNA, using the strand (-) strand as a template to synthesize a single stranded RNA molecule
Where are nucleotides added during elongation
As with DNA replication, nucleotides are added only 3’ end.
What is elongation of RNA fueled by:
The reaction is fueled by hydrolyzing a high energy phosphate bond of the incoming nucleotide.
What happens to RNA polymerase as it moves along DNA in elongation?
When RNA advances, it denatures a new stretch of DNA and allows the previous portion to renature (close).
What is the purpose of denaturation in elongation?
The denaturation exposes a new region of the template so elongation can continue.
When does termination of transcription occur
When RNA polymerase encounters a sequence called a terminator, it falls off the DNA template and releases the newly synthesized RNA.
Components of transcription in bacteria
- (-) strand of DNA
- (+) strand of DNA
- Promoter
- RNA polymerase
- Sigma factor
- Terminator
Three major structures for translation
- mRNA
- Ribosomes
- tRNAs
What is mRNA composed of?
Is composed of nucleotides
What are proteins composed of?
Amino acids
Genetic code
Code that correlates a codon (set of three nucleotides) to one amino acid.
Codon
A series of three nucleotides that code for a specific amino acid.
How many different codons are there?
4^3.
64 different codons
Why are there 64 different codons
Because a codon is a triplet of any combination of the four nucleotides, there are 64 different codons.
Stop codon
Codon that does not code for an amino acid and is not recognized by a tRNA; signals the end of the polypeptide chain.
Signals the end of translation
What signals the end of translation
Stop codon
How many stop codons are there in translation
Three stop codons
How many codons translate to 20 amino acids.
61 codons translate to 20 different amino acids
What does it mean that 61 codons translate to 20 different amino acids
This means that more than one codon can code for a specific amino acid.
What indicates where the coding region begins and ends
The nucleotide sequence of an mRNA molecule indicates where the coding region begins and ends.
Reading frames
Grouping of nucleotides in sequential triplets; an mRNA molecule has three possible reading frames, but only one is typically used in translation.
What happens if translation begins in the wrong reading frame
A very different and generally nonfunctional, protein is synthesized.
Ribosome
A ribosome serves as a translation machine that strings amino acids together to make a polypeptide.
What is a ribosome composed of
Composed of ribosomal RNA (rRNA) and protein.
How does ribosome string amino acids together
It does this by aligning two amino acids and catalyzing the formation of a peptide bond between them.
What does ribosomes do other than stringing amino acids together
Ribosomes also locate key punctuation sequences on the mRNA molecule, such as the points at which synthesis of a particular protein should start and stop.
In prokaryotes, where does the ribosomes begin to assemble
In prokaryotes, the ribosome will begin to assemble at a sequence in mRNA called the ribosome binding site
Ribosome binding site
Sequences of nucleotides in bacterial mRNA to which a ribosome binds; the first time the codon AUG appears after that site, translation starts.
Start codon
Codon at which translation is initiated; in prokaryotes, typically the first AUG after a ribosome binding site.
Where is the start codon typically located in prokaryote
It is the AUG after the ribosome binding site
What direction does ribosome move on mRNA?
Ribosome moves in the 5’ to 3’ direction.
Stop codon
Codon that does not code for an amino acid and is not recognized by tRNA; signals the end of the polypeptide chain.
Where does translation end
Translation ends at stop codon
What are prokaryotic ribosomes composed of:
Prokaryotes ribosomes are composed of a 30S subunit and 50S subunit, each made up of a protein and ribosomal RNA.
What does S stand for in subunit
The S stands for Svedberg unit a measure of size.
What is the role of tRNA
A tRNA is an RNA molecule that carries an amino acid to be used in translation.
Structure of tRNA
Each tRNA is folded into a three dimensional shape held together by hydrogen bonds; a specific amino acid attached at one end
What does the tRNA do
As part of translation, a tRNA base pairs with the appropriate codon in the mRNA molecule, and the ribosome then transfers the amino acid carried by that tRNA onto the end of the newly forming polypeptide.
What does the tRNA do
As part of translation, a tRNA base pairs with the appropriate codon in the mRNA molecule, and the ribosome then transfers the amino acid carried by that tRNA onto the end of the newly forming polypeptide.
Why does recognition between tRNA and mRNA occur
The recognition between the tRNA and the mRNA occurs because each tRNA has an anticodon.
Anticodon
A group of three nucleotides complementary to a codon in the mRNA.
What determines the sequence of amino acids in the protein according to the genetic code
The sequence of codons in the mRNA determines the sequence of amino acids in the protein, according to the genetic code.
What can a tRNA molecule do once it has delivered its amino acid during translation?
Once a tRNA molecule has delivered its amino acid during translation, it can be recycled.
What is an uncharged tRNA
A tRNA not carrying an amino acid.
Three phases of Translation:
- Initiation
- Elongation
- Termination
How does initiation during translation work?
- In prokaryotes, the ribosome begins to assemble at the ribosome binding site, joined by an initiating tRNA that carries a chemically altered form of the amino acid methionine.
- As the ribosome assembles, that initiating tRNA binds to the first AUG after the ribosome binding site and occupies a ribosomal region called the P-site.
Why is it important that the initiating tRNA help position the assembled ribosome relative to the first AUG?
Because the position determines the reading frame used for translating the remainder of that polypeptide.
What are the circumstances that AUG functions as a start codon?
AUG functions as a start codon only when preceded by a ribosome binding site; at other site, it simply encodes methionine.
What are the three relevant sites of a ribosome in translation?
- P site
- A site
- E site
What is Elongation
The elongation phase creates the full length polypeptide.
Steps to elongation (5 steps)
- At start of elongation, the initiating tRNA ( carrying fMet) still occupies the P site. A tRNA that recognizes the next codon on the mRNA then enters and fills the unoccupied A site.
- The ribosome catalyzes the joining of the amino acids carried by the tRNAs and in doing so, transfers the amino acid from the initiating tRNA in the P site to the one carried by the tRNA in the A site.
- The ribosome advances a distance of one codon, a process called translocation, moving along the mRNA in a 5’ to 3’ direction. As this happens the uncharged initiating tRNA is released through the E site to be recycled. The remaining tRNA, which now carries both amino acids, occupies the P site. A tRNA that recognizes the codon in the A site then quickly attaches there. Soon the amino acid chain carried by the tRNA now in the Psite will be transferred to the amino acid carried by the tRNA that just entered the A site.
- The elongation process continues to repeat as the ribosome move along the mRNA in the 5’ to 3’ direction one codon at a time. After each translocation, the uncharged tRNA is released through the E site, a tRNA enters the A site, and the polypeptide chain carried by the tRNA in the P site is transferred to the amino acid carried by the tRNA that just entered the A site. These combined actions elongate the polypeptide chain.
Polyribosome or polysome
The assembly of multiple ribosome attached to a single mRNA molecule.
Termination
The process of translation terminates when the ribosome reaches a stop codon, a codon not recognized by a tRNA.
What exactly happens during termination
At this point, enzymes free the polypeptide by breaking the covalent bond that joined it to the tRNA.
The ribosome falls off the mRNA, dissociating into its two component subunits (30S and 50S). The subunits can then be reused to initiate translation at other sites.
What happens to the ribosome during termination
The ribosome falls off the mRNA, dissociating into its two component subunits (30s and 50s).
Why is gene expression particularly efficient in prokaryotes
In prokaryotes, gene expression is particularly efficient because translation begins while the mRNA molecule is still being synthesized.
Multiple ribosomes can be translating the same mRNA molecule ( true for eukaryotes also).
Components of translation in bacteria
- Anticodon
- mRNA
- Reading frame
- Ribosome
- Ribosome binding site
- rRNA
- Start codon
- Stop codon
- tRNA
What must happen to polypeptides after they are synthesized?
Polypeptides must often be modified after they are synthesized in order to become functional.
Molecular proteins
Protein that helps other proteins fold properly.
Signal sequence
Amino acid sequence that directs cellular machinery to secrete a polypeptide.
A characteristic series of hydrophobic amino acids at their amino terminal end which tags them for transport
When is the signal sequence removed
The signal sequence is removed by membrane proteins during transport.
When is the signal sequence removed
The signal sequence is removed by membrane proteins during transport.
Quick summary of transcription
RNA polymerase synthesizes RNA in the 5’ to 3’ direction using one strand of DNA as a template.
Quick summary of translation
In translation, ribosomes synthesize proteins, using the nucleotide sequence of an mRNA molecule to determine the amino acid sequence of encoded protein. The correct amino acid for a given codon is delivered by tRNAs. After synthesis, many proteins are modified in some way.
How do eukaryotes differ significantly from prokaryotes in transcription and translation?
Eukaryotic mRNA is synthesized in a precursor form, called pre-mRNA.
Unlike prokaryotes, the same mRNA molecule cannot be synthesized and translated at the same time or even in the same cellular location.
Pre-mRNA
A eukaryotic transcript that has not yet had the introns removed.
Transcription in eukaryotes
Shortly after transcription begins, a cap is added to the 5’ end of a pre mRNA, a process called capping.
Capping
In eukaryotic gene expression, adding a methylated guanine derivative to the 5’ end of the mRNA.
What does the cap do during transcription in eukaryotes.
The cap binds specific proteins that stabilize the transcript and enhance translation.
Polyadenylation
In eukaryotic gene expression, adding a series of adenine derivatives to the 3’ end of an mRNA transcript.
What is created during polyadenylation
This creates a poly A tail, which is thought to stabilize the transcript as well as enhance translation.
Splicing
Process that removes introns from an RNA transcript.
Why is splicing necessary
Splicing is necessary because eukaryotic genes are often interrupted by non coding sequences.
Introns
Segment within a gene that must be removed from pre-MRA to create a functional mRNA molecule.
Exons
Portions of eukaryotic genes that will be transcribed and then translated into proteins; interrupted by introns.
What must occur before the mRNA can be translated in eukaryotic cells
The mRNA in eukaryotic cells must be transported out of the nucleus before it can be translated in the cytoplasm.
Difference between prokaryotes and eukaryotes synthesis and translation
Unlike prokaryotes, the same mRNA molecule cannot be synthesized and translated at the same time or even in the same cellular location.
How do ribosomes differ in eukaryotes and prokaryotes
The ribosomes of eukaryotes differ from those of prokaryotes. Whereas the prokaryotic ribosome is 70S, made up of 30S and 50S subunits, the eukaryotic ribosome is 80S, made up of 40S and 60S subunits.
Why are the differences in ribosome structure are medically important
Because certain antibiotics bind to and inactivate bacterial 70S ribosomes, but not 80S ribosomes.
Major differences between eukaryotic and prokaryotic gene expression
- Prokaryote mRNA does not have a cap or a poly A tail.
Eukaryotes- processing of transcript results in mRNA with a cap at the 5’end and a poly A tail at the 3’ end.
- Transcript mRNA doesn’t contain introns for prokaryotes.
Eukaryotes- transcript contains introns, which are removed by splicing.
- Translation of mRNA begins as it is being transcribed.
Eukaryotes- mRNA is transported out of the nucleus so that it can be translated
- MRNA is often Polycistronic; translation usually begins at the first AUG codon that follows a ribosome binding site.
Eukaryotes- mRNA Monocistronic; translation begins at the first AUG.
- Ribosomes are 70S.
Eukaryotes- ribosomes are 80S.
Signal transduction
Is the process that transmit information from outside a cell to inside
Signal transduction
Is the process that transmit information from outside a cell to inside
Signal transduction
Is the process that transmit information from outside a cell to inside
What does signal transduction do
Signal transduction allows the cell to respond to changing environmental conditions.
It’s allows the cells to monitor and react to environmental conditions.
Quorum sensing
Communication between bacterial cells by means of small molecules, permitting the cells to sense the density of nearby cells.
What does quorum sensing allow cells to do
This allows cells to activate genes that are useful only when expressed by a critical mass.
How does quorum sensing work
Quorum sensing involves a process that allows bacteria to talk to each other by synthesizing one or more varieties of extracellular signaling molecules.
How does quorum sensing work in the presence of few cells
When few cells are present, the concentration of a given signaling molecule is very low.
How does quorum sensing work in a high concentration of cells
As the cells multiply in a confined area, the concentration of that molecule increases proportionally.
Only when a signaling molecule reaches a certain level does it change the expression of specific genes.
Two component regulatory system
Important mechanism cells use to detect and react to changes in the environment
Mechanism of gene regulation that uses a sensor and a response regulator
What two proteins is a two component regulatory system consist of
- A membrane spanning sensor
- A response regulator
How does two component regulatory system work
When specific environmental variations occur, the sensor chemically modified a region on its internal portion, usually by adding a phosphate group to a specific amino acid.
The phosphate group is then transferred to a response regulator.
When phosphorylation, the response regulator turns genes either on or off, depending on the system.
Natural selection
The survival and growth of cells best adapted to live a particular environment, can also play a role in gene expression
Antigenic variation
Process by which routine changes occur in a microbial surface antigen.
Pathogens that do this can stay one step ahead of the body’s defenses by altering the very molecules our immune systems must learn to recognize.
Phase variation
The reversible and random alteration of expression of certain bacterial structures such as fimbriae by switching on and off the genes that encode those structures.
What two types of sensing allow microbial cells to respond to changing environmental condition
- Quorum sensing
- Two component regulatory systems
Operon
Group of linked genes whose expression is controlled as a single unit.
One of the most well known operons
Lac operon
Lac operon
Encodes proteins required for transporting and hydrolyzing the disaccharide lactose.
Regulon
Set of related genes transcribed as separate units but controlled by the same regulatory protein.
Global control
The simultaneous regulation of numerous unrelated genes.
Three groups enzymes are categorized in
- Constitutive
- Inducible
- Repressible
Constitutive enzymes
- Are synthesized constantly
-the genes that encode these enzymes are always active
-usually play an important role in central metabolic pathways
Constitutive enzymes are usually involved in what
Constitutive enzymes usually play a role in central metabolic pathways
Example of constitutive enzymes
The enzymes of glycolysis
Inducible enzymes
Are enzymes that are not routinely produced at significant levels;
Their synthesis can be turned on when needed.
Inducible enzymes are often involved in the transport and breakdown of specific energy sources.
Example of inducible enzyme
B galactosidase
B galactosidase
The enzyme that hydrolyzes lactose into component monosaccharides glucose and galactose.
Inducible enzymes are usually involved in what
inducible enzymes are usually involved in the transport and breakdown of specific energy sources
Repressible enzymes
Repressible enzymes are produced routinely, but their synthesis can be turned off when they are not required.
Repressible enzymes are usually involved in what
The enzymes are generally involved in biosynthetic (anabolic) pathways, such as those that produce amino acids.
What quality is important to prevent or facilitate transcription
The methods a cell uses to prevent or facilitate transcription must be readily reversible, allowing cells to control the relative number of transcripts made
Two of the most common regulatory mechanisms are:
- Alternative sigma factors
- DNA binding proteins
Alternative sigma factors
A sigma factor that recognizes promoters controlling genes needed only in non routine situations.
Anti sigma factors
Which inhibit the function of specific sigma factors
What is transcription controlled by
Transcription is controlled by proteins that bind to specific DNA sequences
When a regulatory protein attaches to DNA, it can act as either _____ or _____?
When a regulatory protein attaches to DNA, it can act as either a depressor, high blocks transcription, or an activator, which facilitates transcription.
Repressor
Is a regulatory protein that can block transcription (negative regulation).
How does a repressor block transcription?
It does this by binding to an operator.
When a repressor is bound to an operator, RNA polymerase cannot progress past that DNA sequence.
What happens when a repressor is bound to an operator?
When a repressor is bound to an operator, RNA polymerase cannot progress past that DNA sequence.
What type of proteins are repressors?
Repressors are allosteric proteins
What is a allosteric protein?
Means specific molecules can attach to them and change their shape
Why is the shape of a repressor important?
The shape is important because it affects the repressor’s ability to bind to the operator.
What two types of transcriptional regulatory systems do repressors play a role in:
- Induction
- Repression
Where is the operator located?
The operator is a specific DNA sequence located immediately downstream of a promoter.
What is an allosteric protein?
Means specific molecules can attach to them and change their shape
Induction
The repressor is synthesized as a form that binds to the operator, blocking transcription. When a molecule called an inducer attaches to the repressor, the shape of the repressor changes so that it can no longer attach to the operator. With the repressor unable to bind to DNA, RNA polymerase may transcribe the gene.
Repression
The repressor is synthesized as a form that cannot bind to the operator. However, when a molecule termed a corepressor attaches to the repressor, the corepressor-repressor complex can then bind to the operator, blocking transcription.
Corepressor
Molecule that binds to an inactive repressor, thereby allowing it to function as a repressor.
Inducer
Molecule that activates transcription of certain genes
Inducer applies to a molecule that turns on transcription, either by stimulating the function of an activator or by interfering with the function of a repressor.
Activator
A regulatory protein that facilitates transcription (positive regulation).
In gene regulation, a protein that enhances the ability of RNA polymerase to initiate transcription.
Genes controlled by an activator have what?
Genes controlled by an activator have an ineffective promoter preceded by an activator-binding site.
What happens when the activator binds to the activator binding site?
The binding of the activator to that site enhances the ability of RNA polymerase to initiate transcription from the promoter.
Why are activators allosteric proteins?
When a molecule called an inducer binds to an activator, the shape of the activator changes so that it can then bind to the activator binding site.
Lac operon
Operon that encodes the protein required for the degradation/transport of lactose; it serves as one of the most important models for studying gene regulation.
When is lac operon turned on?
Lac operon is only turned on when glucose is not available but lactose is.
What prevents the expression of the lac operon?
When glucose is available, it prevents the expression of the lac operon genes, ensuring that cells use the most efficiently metabolized carbon source (glucose) first.
What happens when lactose is not available?
The lac operon uses a repressor that prevents transcription when lactose is not available; the repressor binds the operator, blocking RNA polymerase.
RNA interference (RNAi)
Cellular mechanism that targets specific mRNA molecules for destruction by using small RNA fragments to identify it.
More about RNAi
Pg 7.5
Two different molecules used in RNAi
- MicroRNA (miRNA)
- Short interfering RNA (siRNA).
Bioinformatics
Developing and using computer technology to store retrieve, and analyze nucleotide sequence data.
When analyzing a DNA sequence, the —- strand is used to represent the sequence of the corresponding RNA transcript.
(+) strand
Metagenomics
Is the analysis of total microbial genomes in an environment.
What happens when a repressor is bound to an operator?
When a repressor is bound to an operator, RNA polymerase cannot progress past that DNA sequence.
