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Biology - Molecular Genetics


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What is the basic unit of DNA?
The nucleotide, which is composed of deoxyribose (a sugar) bonded to both a phosphate group and a nitrogenous base
What are the two types of bases?
Purines, which are double-ringed, and the single-ringed pyrimidines
What are the purines in DNA?
Adenine and Guanine
What are the pyrimidines?
Cytosine and Thymine
What do nucleotides bond together to form?
What is the 3’ hydroxyl group of the sugar on one nucleotide is joined to what?
The 5’ hydroxyl group of the adjacent sugar by a phosphodiester bond
How many bonds does T always form with A?
Two hydrogen bonds
G always forms how many hydrogen bonds with C?
Three hydrogen bonds
What does this base-pairing form?
It forms rungs on the interior of the double helix that link the two polynucleotide chains together
The strands are positioned how to each other?
They are positioned antiparallel to each other
What does this mean?
The proteins produced (usually enzymes) are said to be repressible since they are normally being synthesized
What is the 5’ end designated as?
It is designated as the end with a free hydroxyl group bonded to the 5’ carbon of the terminal sugar
What is the 3’ end designated as?
The one with a free hydroxyl group attached to the 3’ carbon of the terminal sugar
What is this known as?
It is known as a frameshift mutation
What is semiconservative replication?
During replication the helix unwinds and each strand acts as a template for complementary base-pairing in the synthesis of two new daughter helices
What dos each daughter helix contain?
It contains an intact strand from the parent helix and a newly synthesized strand
Where does replication begin?
It begins at specific sites along the DNA called origins of replication and proceeds in both directions simultaneously
What forms as replication proceeds in a given direction?
A replication fork
What does the enzyme helicase do?
It unwinds the helix
What does single-strand binding protein do?
SSB binds to the single strands and stabilizes them, preventing them from recoiling and forming a double helix
What does DNA gyrase do?
It concurrently introduces negative supercoils to relieve the tension created during unwinding
What is a primer chain?
It is usually several nucleotides long and composed of RNA
What does it do?
It has an active site that binds to both the amino acid and its corresponding tRNA, catalyzing their attachment to form an aminoacyl-tRNA complex
What does the RNA polymerase, primase, do?
It synthesizes the primer, which binds to a segment of DNA to which it is complementary and serves as the site for nucleotide addition
What does the first nucleotide bind to?
It binds to the 3’ end of the primer chain
Which direction does DNA synthesis proceed in?
It proceeds in the 5’ ‡ 3’ direction and is catalyzed by a group of enzymes collectively known as DNA polymerases
What is the double-stranded DNA ahead of the DNA polymerase unwound by?
A helicase, and SSB again keeps the unwound DNA in a single-stranded form so that both strands can serve as templates
What is the leading strand?
One of the daughter strands
What is the other strand called?
It is called the lagging strand
What happens to the leading strand?
It is continuously synthesized by DNA polymerase in the 5’ ‡ 3’ direction
How is the lagging strand synthesized?
It is synthesized discontinuously in the 5’ ‡ 3’ direction as a series of short segments known as Okazaki fragments
What is the overall direction of growth of the lagging strand?
It occurs in the 3’ ‡ 5’ direction
What covalently links the fragments?
DNA ligase
How many strands is RNA usually?
It is usually single stranded
What are the several types of RNA?
mRNA, tRNA, rRNA, and hnRNA
What is messenger RNA?
mRNA carries the complement of a DNA sequence and transports it from the nucleus to the ribosomes, where protein synthesis
What is monocistronic?
What is tRNA?
It is found in the cytoplasm and aids in the translation of mRNA’s nucleotide code into a sequence of amino acids
What does tRNA bring amino acids to?
It brings them to the ribosomes during protein synthesis
How many types of tRNA are there?
Approximately one type of tRNA for each amino acid, so about 40
What is rRNA?
It is a structural component of ribosomes and is the most abundant of all RNA types
Where is it synthesized?
In the nucleolus
What is hnRNA?
It is a large ribonucleoprotein complex that is the precursor of mRNA
What is transcription?
It is the process whereby information coded in the base sequence of DNA is transcribed into a strand of mRNA
What is mRNA synthesized from?
A DNA template in a process similar to DNA replication
Where does DNA helix unwind?
It unwinds at the point of transcription, and synthesis occurs in the 5’ ‡ 3’ direction, using only one DNA strand as a template
What is this template known as?
The antisense strand
What is mRNA synthesized by?
The enzyme RNA polymerase, which must bind to sites on the DNA called promoters to begin RNA synthesis
What stops synthesis?
It continues until the polymerase encounters a termination sequence, which signals RNA polymerase to stop transcription, thus allowing the DNA helix to reform
What are exons?
They are coding sequences
What are introns?
Noncoding sequences
What is RNA initially transcribed by?
A precursor molecule hnRNA, which contains both introns and exons
What happens during hnRNA processing?
The introns are cleaved and removed, while the exons are spliced to form a mRNA molecule coding for a single polypeptide
Where does processing occur?
Within the nucleus, and is also necessary for tRNA and rRNA production
What is the triplet code?
The base sequence of mRNA is translated as a series of triplets, otherwise known as codons
What does a sequence of three consecutive bases code for?
A particular amino acid
How many different codons are possible?
64 codons
What is the fact that most amino acids have more than one codon specifying them?
This property is referred to as the degeneracy or redundancy of the genetic code
What is translation?
The process whereby mRNA codons are transplated into a sequence of amino acids
Where does translation occur?
In the cytoplasm and involves tRNA, ribosomes, mRNA, amino acids, enzymes, and other proteins
What does tRNA do?
It brings amino acids to the ribosomes in the correct sequence for polypeptide synthesis
What does it recognize?
It recognizes both the amino acid the mRNA codon
What is the dual function reflected by?
Its three-dimensional structure: one end contains a three-nucleotide sequence
What is the sequence called?
The anticodon, which is complementary to one of the mRNA codons
What does each amino have?
It has its own aminoacyl-tRNA synthetase
What are ribosomes?
They are composed of two subunits, consisting of proteins and rRNA
How many binding sites to ribosomes have?
They have three binding sites: one for mRNA, and two for tRNA
What are the two sites for tRNA called?
The P site, and the A site
What does the P site do?
It binds to the tRNA attached to the growing polypeptide chain
What does the A site do?
It binds to the incoming aminoacyl-tRNA complex
How does polypeptide synthesis work?
It can be divided into three distinct stages
What are they?
They are smaller circular rings of DNA, which contain accessory genes
Do they require energy?
All three do
What are they mediated by?
What happens with initiation?
Synthesis begins when the small ribosomal subunit binds to the mRNA near its 5’ end in the presence of proteins called initiation factors
What does the ribosome scan?
It scans the mRNA until it bonds to a start codon (AUG)
What does the initiator aminoacyl-tRNA complex do?
Methionine-tRNA, the initiator complex, base pairs with the start codon
What does the large ribosomal unit do?
It binds to the small one, creating a complete ribosome with the met-tRNA complex sitting in the P site
How does elongation work?
Hydrogen bonds form between the mRNA codon in the A site and its complementary anticodon on the incoming aminoacyl-tRNA complex
What does the enzyme peptidyl transferase do?
It catalyzes the formation of a peptide bond between the amino acid attached to the tRNA in the A site and the met attached to the tRNA in the P site
What happens following peptide bond formation?
A ribosome carries uncharged tRNA in the P site and peptidyl-tRNA in the A site
What is the cycle completed by?
It is completed by translocation
What occurs?
The ribosome advances 3 nucleotides along the mRNA in the 5’ ‡ 3’ direction
What happens in a concurrent action?
The uncharged tRNA from the P site is expelled and the peptidyl-tRNA from the A site moves into the P site
What happens to the empty A site?
It is ready for entry of the aminoacyl-tRNA corresponding to the next codon
How does termination work?
It terminates when one of three special mRNA termination codons (UAA, UAG, UGA) arrives in the A site
How does this work?
These codons signal for ribosome to terminate translation
What do they do?
A protein called release factor binds to the termination codon, causing a water molecule to be added to the polypeptide chain
What does this precipitate?
It precipitates the release of the polypeptide chain from the tRNA and the ribosome itself
What does the ribosome do then?
It dissociates into its two subunits
What happens frequently?
Many ribosomes simultaneously translate a single mRNA molecule, forming a structure known as a polyribosome
What happens during and after polypeptide release?
It assumes the characteristic conformation determined by the primary sequence of amino acids
What happens with disulfide bonds?
They can form within or between polypeptide chains
What else happens post-translation?
Modification can be made to the polypeptide before it becomes a functional protein
For example?
There might be cleavages and or additions at the terminal ends of the chain
What is mutation?
A change in the base sequence of DNA that may be inherited by offspring
What are the three common types of mutations?
Base-pair substitutions, base-pair insertions, and base-pair deletions
What happens with point mutations?
It occurs when a single nucleotide base is substituted by another
What happens if the substitution occurs in a noncoding region, or if the substitution is transcribed into a codon that codes for the same amino acid?
There will be no change in the amino acid sequence
What if the substitution changes the sequence?
The result can range from insignificant to lethal, depending on the effect the substitution has on the protein
What is an example of a single base-pair substitution?
Sickle cell anemia
What about base-pair insertions and deletions?
They involve the addition or loss of nucleotides, respectively
What kinds of effects do they have?
They usually have more serious effects on the protein coded for, since nucleotides are read as a series of triplets
What does the addition or loss of a nucleotide cause?
It changes the reading frame of the mRNA
What happens to the protein?
If synthesized at all, will most likely be nonfunctional
What is mutagenesis?
It is the creation of mutations
What can it be caused by?
Internal genetic mistakes or by external cancer-causing agents called mutagens
How do internal mistakes occur?
They occur during DNA replication
What does this result in?
It results in gene mutations and dysfunctional proteins
What are physical mutagens?
They are things such as X rays and ultraviolet radiation
What are chemical mutagens?
Base analogs
How can DNA act as a mutagen?
Mobile pieces of DNA called transposons can insert themselves in genes and cause mutation
What does a viral genome contain?
Anywhere from several to several hundred genes
What does it consist of?
Either double stranded or single stranded DNA or RNA
Are viruses specific?
They are highly specific with respect to host selection and can be generally grouped into plant viruses, animal viruses, and bacteriophages
How can a virus infect a host cell?
It can only infect one that has a surface receptor for the virus’ capsid (protein coat)
How does it enter the host cell?
Via a variety of mechanisms
How do some enter?
Some introduce only their nucleic acid into the host cell’s cytoplasm
What about others?
Other enter the host cell entirely
What are DNA containing viruses?
Viral DNA is replicated and viral mRNA transcribed inside the host cell’s nucleus, using the host’s DNA polymerases, RNA polymerases, and nucleotide pool
Do any DNA viruses replicate and transcribe in the cytoplasm?
A few do
How do they work?
They must bring their own DNA and RNA polymerases with them
How is Viral RNA replicated and transcribed?
In the host cell’s cytoplasm
What does RNA replicase do?
It transcribes new RNA from an RNA template
What do some viruses do with RNA replicase?
Some bring it with them into the host
A portion of viral RNA functions as mRNA, which is translated into RNA replicase immediately after entering the hose cell
What are retroviruses?
They are a special group of RNA viruses that use their genome as a template for DNA synthesis rather than for RNA synthesis
How is DNA synthesized?
By the enzyme reverse transcriptase
What happens to retroviral DNA?
It becomes integrated into the host DNA
What happens when viral DNA becomes integrated into host DNA?
It is called a provirus or prophage after that
What happens to the proviral DNA later?
It is transcribed into mRNA needed for prophage assembly
What happens to viral mRNA transcribed from viral nucleic acid?
It is translated into the polypeptide chains that compose the viral protein coats with the aid of the host cell’s tRNA, amino acids, ribosomes, and enzymes
How do viral progeny assemble?
They self-assemble
What happens to the protein-nucleic acid configuration?
It forms either spontaneously or with the aid of viral enzymes
What happens once viral progeny are assembled?
They may be released either by lysis of the host cell, or by extrusion, a process similar to budding
What happens in extrusion?
The progeny are enclosed in vesicles derived from the host cell membrane
What does this permit?
It permits viral replication without killing the host cell
What is the process of viral replication and extrusion in animal viruses called?
A productive cycle
What is a bacteriophage?
It infects its host bacterium by attaching to it, boring a hole through the bacterial cell wall, and injecting its DNA, while its protein coat remains attached to the cell wall
What happens within the host?
Within the host, the bacteriophage enters either a lytic cycle or a lysogenic cycle
What happens in the lytic cycle?
The phage DNA takes control of the bacterium’s genetic machinery and manufactures numerous progeny
What happens to the bacterial cell then?
It bursts (lyses), releasing new virions
What are each capable of?
Each is capable of infecting other bacteria
What are bacteriophages that replicate by the lytic cycle, killing their host cells, called?
What happens if the bacteriophage does not lyse its host cell?
It becomes integrated into the bacterial genome in a harmless form (provirus)
What happens to it then?
It lies dormant for one or more generations
Then what?
It may stay integrated indefinitely, replicating along with the bacterial genome
What can cause the provirus to reemerge and enter a lytic cycle?
It can be spontaneously, or as a result of environmental circumstances such as radiation, ultraviolet light, or chemicals
What are bacteria containing proviruses resistant to?
Further infection (super infection) by similar phages
What does the bacterial genome consist of?
It consists of a single circular chromosome located in the nucleoid region of the cell
What are plasmids?
They are what many bacteria also contain
What are episomes?
They are plasmids that are capable of integration into the bacterial genome
What happens as soon as a small portion of newly synthesized mRNA separates from its DNA template?
Translation begins
What is polycistronic?
It is what a strand of prokaryotic mRNA may be
Where does replication of the bacterial chromosome begin?
At a unique origin of replication and proceeds in both directions simultaneously
What direction is DNA synthesized?
In the 5’ ‡ 3’ direction
What is the rate of replication?
It occurs at approximately 500 nucleotide additions per second
How do bacterial cells reproduce?
By binary fission and proliferate very rapidly under favorable conditions
What type of process is binary fission?
What are the three mechanisms for increasing genetic variance of a bacterial population?
Transformation, conjugation, and transduction
What is transformation?
It is the process by which a foreign chromosome fragment (plasmid) is incorporated into the bacterial chromosome via recombination, creating new inheritable genetic combinations
What is conjugation?
It can be described as sexual mating in bacteria
What is a cytoplasmic conjugation bridge?
It is formed between two cells and genetic material is transferred from the donor male (+) type to the recipient female (-) type
How is the bridge formed?
Through appendages called sex pili
Where are they found?
On the donor male
What are sex factors?
They are plasmids that allow bacteria to be capable of forming pili and conjugating
What is the best sex factor known?
The F factor in E. coli
How does it work?
Bacteria possessing the plasmid are termed F+ cells, those without it are called F- cells
What happens during conjugation between an F+ and F- cell?
The F+ cell replicates it F factor and donates the copy to the recipient, converting it to an F+ cell
What about plasmids that do not induce pili formation?
They may transfer into the recipient cell along with the sex factor
What happens sometimes to the sex factor?
It can become integrated into the bacterial genome
What happens during conjugation to the entire bacterial chromosome?
It replicates and begins to move from the donor cell into the recipient cell
When does the conjugation bridge break?
It usually breaks before the entire chromosome is transferred, but the bacterial genes that enter the recipient cell can easily recombine with the bacterial genes already present to form novel genetic combinations
What are these bacteria called?
Hfr cells, meaning that they have a high frequency of recombination
What is transduction?
It is when fragments of the bacterial chromosome accidentally become packaged into viral progeny produced during a viral infection
What do these virions do?
They may infect other bacteria and introduce new genetic arrangements through recombination with the new host cell’s DNA
What is this process similar to?
It is similar to conjugation, and may reflect an evolutionary relationship between viruses and plasmids
How does the regulation of gene expression enable prokaryotes to control their metabolism?
Regulation of transcription is based on the accessibility of RNA polymerase to the genes being transcribed
What is it directed by?
An operon
What does an operon consist of?
It consists of structural genes, an operator gene, and a promoter gene
What do structural genes contain?
They contain sequences of DNA that code for proteins
What is the operator gene?
It is the sequence of nontranscribiable DNA that is the repressor binding site
What is the promoter gene?
It is the noncoding sequence of DNA that serves as the initial binding site for RNA polymerase
What is the regulator gene?
It codes for the synthesis of a repressor molecule that binds to the operator and blocks RNA polymerase from transcribing structural genes
How may regulation take place?
Via inducible systems or repressible systems
What are inducible systems?
They are systems that require the presence of a substance, called an inducer, for transcription to occur
What are repressible systems?
They are in constant state of transcription unless a corepressor is present to inhibit transcription
What happens in an inducible system?
The repressor binds to the operator, forming a barrier that prevents RNA polymerase from transcribing the structural genes
How long is the repressor active?
It is active until it binds to the inducer
What is needed for transcription to occur?
An inducer must bind to the repressor, forming an inducer-repressor complex
What is this complex?
It cannot bind to the operator, thus permitting transcription
What are the proteins synthesized?
They are thus said to be inducible
What do structural genes code for?
They typically code for an enzyme
What is the inducer?
It is usually the substrate, or a derivative of the substrate, upon which the enzyme normally acts
What happens when the substrate (inducer) is present?
Enzymes are synthesized
What about when it’s not present?
Enzyme synthesis is negligible
In this manner, what occurs?
Enzymes are transcribed only when they are actually needed
What is an example of an inducible system?
The lac operon is one
What about repressible systems?
The repressor is inactive until it combines with the corepressor
What does the repressor bind to?
The operator
What does this prevent?
It prevents transcription only when it has formed a repressor-corepressor complex
What are corepressors often?
They are often the end-products of the biosynthetic pathways they control
How long does transcription and translation occur?
Until the corepressor is synthesized
What is an example of a repressible system?
The trp operon

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