Flashcards in Unit 5 Test Deck (117):
What is the accepted theory for DNA replication?
Semiconservative, where each DNA molecule is made from one old and one new strand.
During DNA synthesis, are nucleotides added to the 3' or 5' end?
Nucleotides are added to the 3' end of the growing new strand from the 5' end.
What are deoxyribonucleoside triphosphates (dNTPs)?
The raw materials for DNA synthesis (dATP, dTTP, dTCP, and dTGP).
How is the 3-phosphate structure important for the function of dNTPs?
During DNA synthesis, the two outer phosphate groups are released, which creates the energy needed to form the phosphodiester bonds between the remaining phosphate group and the 3' Carbon.
What is used to catalyze the additions of nucleotides to the growing DNA strand?
Where does DNA replication begin?
The origin of replication (ori).
What is the replication bubble?
The opening of DNA where replication is occurring.
What are the replication forks?
The two "sides" of the replication bubble that the replicated DNA will grow towards.
How do prokaryotic and eukaryotic origins of replication differ?
Prokaryotes only have one origin of replication, while eukaryotes have many.
Which enzyme is responsible for unwinding each replication fork?
What is topoisomerase?
The enzyme responsible for removing the tension created by Helicase.
What is the purpose of a primer?
DNA polymerase is unable to start replication by itself, so primer is necessary for beginning replication.
What is a primase?
The enzyme that lays down the primer.
What is the leading strand?
The strand of DNA that grows continuously towards the replication fork.
What is the lagging strand?
The strand of DNA that grows away from the replication fork, and must therefore have new primers constantly added to it.
What are Okazaki fragments?
The stretches of DNA in between primers.
How are Okazaki fragments joined together?
DNA polymerase I will replace the primer with DNA, and DNA ligase will catalyze the creation of the bond that connects the fragments.
Why will new chromosomes have a small amount of single-stranded DNA at each end?
When the last DNA primer is removed, no DNA can be synthesized to replace it because there is no 3' end to extend. This makes it so that the original strand is slightly longer than the new strand.
How do cells fix the problem of shortening DNA?
Telomeres will be added to the ends of chromosomes through telomerase.
What are telomeres?
Strings of repetitive nucleotide sequences that don't actually hold any genetic information.
What are the two major repair mechanisms for DNA replication?
Proofreading and mismatch repair.
What is proofreading?
When DNA polymerase inserts the wrong nucleotide into the synthesizing strand of DNA, the polymerase will immediately take out the incorrect nucleotide and try again.
What is mismatch repair?
When an error is noticed in post-replicated DNA, repair proteins will remove the mismatched base from the strand, and a DNA polymerase will add the correct bases.
What is the polymerase chain reaction (PCR)?
A cyclic process where artificial primers will repeatedly start the synthesis of new DNA strands, allowing researchers to make multiple copies of short DNA sequences in a test tube.
What is the central dogma?
The flow of information in a cell (from DNA to RNA to proteins).
What is transcription?
When the information in a DNA sequence is copied into a complementary RNA sequence.
What is translation?
When an RNA sequence is used to create an amino acid sequence of a polypeptide.
What is the difference between the coding strand and the template strand?
The coding strand will exactly resemble the RNA strand (except T's become U's), and the template strand is what is being transcribed.
What is the primary difference between RNA polymerase and DNA polymerase?
Unlike DNA polymerase, RNA polymerase does not need a primer.
What are the three processes that make up transcription?
Initiation, elongation, and termination.
What are the components of transcription initiation?
The promoter sequence, the unwinding, and the promoter release.
What is the promoter sequence?
A sequence of DNA that tells the cell where a gene starts and where RNA polymerase will first bind.
What is the unwinding sequence?
When RNA polymerase unwinds the DNA.
What is promoter release?
RNA will takes a few tries before it is committed (10 nucleotides). Once committed, elongation will begin.
What are the three main "jobs" of RNA polymerase during elongation?
Unwinding/reannealing, dissociation, and proofreading.
What is unwinding and reannealing?
RNA polymerase unwinds the DNA in front of it and reanneals the DNA behind it.
What is dissociation?
RNA polymerase ensures that the RNA does not stay attached to the DNA.
In what direction does RNA polymerase read the template strand?
3' to 5'.
In what direction is RNA synthesized?
5' to 3'.
What happens during transcription termination?
RNA polymerase dissociates completely from the DNA.
What is RNA processing?
Pre-mRNA is modified to make it into a mature mRNA transcript.
What is capping?
Once RNA polymerase is committed, a guanine nucleotide and a methyl group will be added to the 5' end (GTP-cap).
What is Polyadenylation?
The adding of 200 adenine nucleotides to the 3' end of the mRNA.
What is the poly-a-tail?
The 200 adenine nucleotides at the end of the mRNA.
What are exons?
Coding regions of mRNA
What are introns?
Noncoding regions of mRNA
Why does mRNA have introns?
It allows for alternative splicing
What is splicing?
Removing noncoding parts of the mRNA and gluing back together the coding parts.
What are snRNPs?
Small nuclear ribonucleoprotein particles that bind to consensus sequences.
What are consensus sequences?
Short stretches of DNA with very little variation that occur at the boundary between introns and exons, and indicate where splicing will occur.
How are spliced introns "glued" back together?
The snRNPs will form a large complex called the spliceosome, which joins the ends of the introns together.
What is a codon?
A series of sequential, non-overlapping, three-letter "words" that code for amino acids.
What are missense mutations?
Point mutations that result in a change in the amino acid sequence.
What are nonsense mutations?
Point mutations that result in a premature stop codon.
What is a start codon?
The codon that acts as the initiation signal for translation.
What is a stop codon?
A codon that acts as the termination signal for translation.
What is the role of tRNA?
It brings amino acids to the ribosome that correspond to various codons, and creates polypeptide bonds that allow the amino acid chain to grow.
What is the anticodon?
Three bases at about the midpoint of the tRNA strand that are complementary to the mRNA codon for the particular amino acid that the tRNA carries.
What is the site for protein synthesis?
What does it mean for tRNA to be "charged"?
A "charged" tRNA is one bonded to its specific amino acid.
What is the enzyme responsible for catalyzing the bond between tRNA and the amino acid?
What are ribosomes made out of?
Various proteins and RNA.
What are the three binding sites in a ribosome?
The A(mino acid) site, the P(olypeptide) site, and the E(xit) site.
What are the three steps of translation?
Initiation, elongation, and termination.
What is the first step of translation initiation?
The initiator tRNA enters at the P-Site
What is the second step of translation initiation?
The next tRNA enters at the A site
What is the third step of translation initiation?
The amino acids are connected by a peptide bond
What happens during translation elongation?
The ribosome moves forwards in the 5' to 3' direction while the mRNA stays stationary
What is the most common stage for regulation of gene expression to occur?
What is a signal sequence?
A short stretch of amino acids at the end of a polypeptide that indicate where in the cell that polypeptide belongs.
What are the three main protein modifications?
Proteolysis, glycosylation, and phosphorylation.
What is proteolysis?
When a polypeptide chain is cut to allow the fragments to form different shapes.
What is glycosylation?
When carbohydrates are added to protein to form glycoproteins, allowing the glycosylated proteins to be more easily targeted and recognized.
What is phosphorylation?
When a phosphate group is added to a protein via a kinase in order to change the shape of the protein, which can either activate or inhibit it.
How does an activator operate?
An activator will bind to the activator binding site on a particular gene, which will stimulate transcription.
How does a repressor operate?
A repressor will bind to the repressor binding site on a particular gene, which will block transcription.
What are the two types of transcription factors?
Activators and repressors.
What is an operon?
A unit of genetic information made out of the promoter, the operator, and the set of genes waiting to be transcribed.
What is the difference between an inducable and a repressable operon?
A repressible operon is typically "on" and can be repressed, while an inducable operon is typically "off" and can be turned on.
What genes does the lac operon control?
Three proteins responsible for the metabolism of lactose.
On the lac operon, does a repressor or an activator bind to the operator? Why?
A repressor binds to the operator, and is only removed when lactose is present. This is so that prokaryotes will only produce the proteins responsible for lactose metabolism when lactose is actually present.
Is the lac operon inducable or repressible?
Inducible, since the operon is typically "off" but can be turned "on" in the presence of lactose.
What is the corepressor?
The molecule that binds to the repressor, causing it to change shape and bind to the operator.
What does bacteria prefer: lactose or glucose?
Glucose, since it is used in respiration
In what environmental conditions would an activator bind to an operon that produces glucose synthesis enzymes?
If glucose levels are low.
How does the activator of a glucose operon function?
If glucose is low, cAMP is high, and will alter the shape of the activator so that it is able to bind.
What does the trp operon control?
The trp operon codes for enzymes involved in the tryptophan synthesis pathway.
On the trp operon, does a repressor or an activator bind to the operator? Why?
A repressor will bind to the trp operon, but only when tryptophan is present in the environment. This is so that the prokaryote will only produce tryptophan synthesis enzymes in the absence of tryptophan.
Is the trp operon inducable or repressible?
Repressible, since the operon is typically "on", but can be turned "off" in the presence of tryptophan.
Do inducable systems generally control catabolic or anabolic pathways?
Catabolic, since they will only be turned on when the substrate is availible.
Do repressible systems generally control catabolic or anabolic pathways?
Anabolic, since they will be turned on until the concentration of the product becomes sufficient.
What is a constitutive gene?
Genes that are consistently transcribed, typically in low levels.
What is a sigma factor?
A protein that can bind to RNA polymerase and direct to polymerase to specific promoters.
What is bacterial transformation?
When bacteria takes up DNA through the cell membrane.
What is cell competence?
A cell's ability to take up extracellular DNA from its environment.
How are cells made to be competent in a lab?
They're suspended in a calcium chloride solution to neutralize the cell wall and shocked with heat.
What is bacterial conjugation?
The process where DNA from one cell is transferred to another cell through cell-to-cell contact.
What are the F+ and F- cells of bacteria?
F+ is the donor cell during conjugation, and will extend its pilus to the F- cell, which is the recipient.
What is bacterial transduction?
The process by which foreign DNA is introduced into a cell through a virus.
What is the lyctic cycle?
A virus infects a host cell and turns it into a virus-producing factor. The cell will then lyse, releasing all of the new viruses into the environment.
What is the lysogenic cycle?
A dormant phase before the lyctic cycle where the viral genome becomes incorporated into the host genome and will be replicated during mitosis.
What are the differences between eukaryotic and prokaryotic gene regulation?
Prokaryotes have one type of RNA polymerase while eukaryotes have three, prokaryotes' only transcription factor is sigma while eukaryotes have many transcription factors, and eukaryotic DNA is wrapped into a nucleosome while prokaryotic DNA is not.
What is a transcription factor?
A regulatory protein that determines whether or not a gene is active.
In eukaryotic cells, where does RNA polymerase bind?
The TATA box, which is the core promoter sequence for RNA polymerase.
What is the purpose of general transcription factors?
They alter the DNA in a way that makes it suitable for RNA polymerase to bind.
What is TFIID?
The first transcription factor to come to the promoter sequence.
What happens after TFIID has bonded to the TATA box?
New transcription factors will bind to TFIID until RNA polymerase is able to bind as well.
What are enhancers?
DNA sequences that bind activators of transcription.
What are silencers?
DNA sequences that bind repressors of transcription.
How do eukaryotes coordinate the regulation of several genes if their genes are dispersed throughout the genome?
Genes with similar functions will have the same regulatory sequences and therefore bind to the same transcription factors.
How can scientists artificially insert a gene of interest into a plasmid?
How does acetylation work?
An acetyl group bonded to a histone protein will cause the protein to "relax", allowing transcription factors to bind to the coiled DNA.
How does methylation work?
A methyl group bound to a specific gene will repress transcription of that gene until the methyl group is removed by demethylase.
What are epigenetic changes?
Reversible, non-sequence-specific alterations to either DNA or packaging proteins.
How does alternative splicing work?
During the splicing of introns, exons can be spliced as well, resulting from different mRNA sequences corresponding to the same strand of DNA.
What is microRNA?
microRNA is a noncoding region of DNA transcribed into RNA, which is responsible for degrading unneeded target mRNA.