Unit 5 - DNA , Biotechnology and Protein Synthesis Flashcards
1
Q
Explain the role of DNA polymerase in DNA replication.
A
DNA polymerase add nucleotides to form a complementary strand of DNA, but it can only add nucleotides to the 3’ end of an existing strand. Therefore, to start at the 5’ end, it must ad nucelotides to an RNA primase.
2
Q
What are the steps of DNA replication?
A
DNA is unzipped, and a new strand is composed of complementary bases by RNA polymerase. On the lagging strand, Okazaki fragments are small chunks of complementary bases. These are then connceted by DNA ligase.
3
Q
Describe the structure of a double helix.
A
The double helix looks like a long twisted ladder.
4
Q
What is gel electrophoresis?
A
Gel electrophoresis separates DNA fragments according to their molecular weight. Because DNA is negatively charded, it moves towards the positive end.
5
Q
What is euchromatin?
A
Euchromatin is genetic material in a loose form, with active genes available for transcription.
6
Q
What is an exon?
A
Exons are coding regions of DNA.
7
Q
What is a frameshift mutation?
A
A frameshift mutation is a genetic mutation caused by insertions or deletions of a number of nucleotides in a DNA sequence that is not divisible by three.
8
Q
How is gene expression regulated?
A
Operons can regulate gene expression.
9
Q
What is genetic engineering?
A
Genetic engineering is the branch of technology that produces new organisms or products by transferring genes between cells.
10
Q
What function does a guanine cap serve?
A
The 5’G cap serves to protect the mRNA strand from degradation by enzymes.
11
Q
What is the start codon in eukaryotes?
A
AUG (MET)
12
Q
What is the role of transcription factors?
A
Transcription factors control the transfer of genetic information from DNA to RNA by binding to specific DNA sequences.
13
Q
What are the three steps of protein synthesis?
A
Transcription, RNA processing, and translation
14
Q
What occurs at the P site of a ribosome?
A
At the P site, an initiator tRNA serves to activate translation and occupies the site.
15
Q
What occurs at the E site of a ribosome?
A
At the E site, the uncharged tRNA molecule exits, after giving away its amino acids.
16
Q
What is a mutation and what are the two groups of mutations?
A
All mutations fall into two groups: base substitutions and gene rearrangements. A mutation is a change in the nucleotide sequence of an organism’s DNA or in the DNA or RNA of a virus.
17
Q
What are nucleotides the building blocks of?
A
Nucleotides are the building blocks of nucleic acids, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and one or more phosphate groups.
18
Q
What is the role of rRNA?
A
A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more ribosomal RNAs (rRNAs). Ribosomal RNA genes are transcribed, and the RNA is processed and assembled with proteins imported from the cytoplasm. rRNA is essential for protein synthesis of all living organisms.
19
Q
What is the function of RNase and what does it stand for?
A
RNase stands for ribonuclease. RNase is a type of nuclease that catalyzes the degradation of RNA into smaller components.
20
Q
What is the role of RNAi and what does it stand for?
A
RNA interference is a technique used to silence the expression of selected genes. RNAi uses synthetic double-stranded RNA molecules that match the sequence of a particular gene to trigger the breakdown of the gene’s messenger RNA.
21
Q
Explain the function of okazaki fragments in DNA replication.
A
An okazaki fragment is a short segment of DNA synthesized away from the replication fork on a template strand during DNA replication. Many such segments are joined together to make up the lagging strand of newly synthesized DNA.
22
Q
Explain the components of an operon.
A
An operon is a unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway.
23
Q
What is the function of an operator?
A
In bacterial and phage DNA, an operator is a sequence of nucleotides near the start of an operon to which an active repressor can attach. The binding of the repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon.
24
Q
Explain primer in DNA replication.
A
Primer is a short stretch of RNA with a free 3’ end, bound by complementary base pairing to the template strand and elongated with DNA nucleotides during DNA replication.
25
What is a plasmid and how is it used in DNA cloning?
A plasmid is a small, circular, double-stranded DNA molecule that carries accessory genes separate from those of a bacterial chromosome. In DNA cloning, it is used as vectors carrying up to about 10,000 base pairs of DNA. Plasmids are also found in some eukaryotes, such as yeasts.
26
What is the role of snRNPs in splicing?
snRNPs are small nuclear ribonucleoproteins. They are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.
27
Describe an example of a corepressor.
Tryptophan functions in the trp operon as a corepressor, a small molecule that cooperates with a repressor protein to switch an operon off.
28
Explain the function of miRNAs and how they are made.
miRNAs are capable of binding to complementary sequences in mRNA molecules. The miRNAs are made from longer RNA precursors that fold back on themselves, forming one or more short double-stranded hairpin structures, each held together by hydrogen bonds.
29
What is the function of an inducer?
An inducer inactivates the repressor. For the lac operon, the inducer is allolactose, an isomer of lactose formed in small amounts from lactose that enters the cell.
30
What is CAP and what does it function as?
The regulatory protein, called catabolite activator protein (CAP), is an activator, a protein that binds to DNA and stimulates transcription of a gene.
31
Describe the anti-parallel structure of DNA.
DNA molecules have two strands that form a double helix. The two sugar-phosphate bacakbones run in opposite 5'-->3' directions from each other, which is referred to as antiparallel.
32
Explain the role of anticodons during the process of translation, and give an example.
As it arrives at a ribosome, a tRNA molecule carries a specific amino acid at one end. At the other end of the tRNA is an anticodon, which a nucleotide triplet that base-pairs with a complementary condon on the mRNA. For example, the mRNA codon GGC base-pairs with a tRNA CCG anticodon. As the mRNA molecule moves through a ribosome, glycine will be added to the polypeptide chain after translation.
33
Explain how biotechnology is used to express a gene of interest in any species.
DNA can be artificially made so an organism can express a gene that it originally did not have. Several components of different plasmids, such as the pBAD and rfp genes from the pKAN-R plasmid and the ori site and ampR and ara C genes of the pARA plasmid, can be combined and rearranged to form a recombinant plasmid that expresses the gene of interest.
34
Explain the role of cAMP as a second messenger during signal transduction, as well as its role in positive gene regulation.
Many signaling pathways also involve small, non-protein, water-soluble molecules or ions called second messengers. Adenylyl cyclase converts ATP to cAMP in response to an extracellular signal. The immediate effect of cAMP is usually the activation of protein kinase A, which phosphorylates various other proteins. In terms of gene regulation, cAMP accumulates when glucose is scarce. cAMP binds to the regulatory protein CAP to activate it, which increases the rate of trancription of the lac genes.
35
What are chromosomes, and what do all eukaryotic chromosomes consist of?
Chromosomes are located in the nucleus, and they are structures that carry genetic information. Each eukaryotic chromosome consists of one very long, linear DNA molecule associated with many proteins. The DNA molecule carries genes that specify an organism's inherited traits.
36
Give a brief overview of gene cloning, as well as what a cloning vector is.
Gene cloning is the multiple copies of a single gene. First, a gene is inserted into a plasmid. The plasmid is then put into a bacterial cell, which is then grown in culture to form a clone of cells containing the "cloned" gene of interest. Proteins are then expressed from this gene of interest, and basic research can be done on these proteins or the gene itself. Genes are cloned in plasmids; a cloning vector is a DNA molecule that carries foreign DNA into a host cell, where it replicates.
37
How are codons along an mRNA molecule decoded/translated into amino acids that make up a polypeptide chain?
Codons are nucleotide triplets that are read by the translation machinery in the 5'-->3' direction along mRNA. Each codon specifies which one of the 20 amino acids will be incorporated in a polypeptide. The number of nucleotides must be three times the number of amino acids in the protein made.
38
Give an example of a corepressor and how it works.
An example of a corepressor is tryptophan, as it cooperates with a repressor protein to turn an operon off. As tryptophan accumulates, more tryptophan molecules associate with trp repressor molecules, which then bind to the trp operator. This blocks transcription, as production of the tryptophan pathway enzymes is shut down.
39
Describe the monomers and function of DNA.
DNA is made of nucleotides, each of which has a phosphate group, a deoxyribose sugar, and one of four types of nucleotide bases. DNA carries the genetic/hereditary information of an organism, as well as the instructions needed for an organism to develop, survive and reproduce. Sequences of DNA must be converted into messages (mRNA during transcription) that can be used to make proteins (during translation).
40
Describe the effect of DNA methylation, as well as how it accounts for genomic imprinting in mammals.
During DNA methylation, methyl groups are added to DNA, which modifies its function. DNA methylation can act to reduce gene transcription since the DNA is more tightly packed together, making it more difficult for DNA to be transcribed. In terms of genomic imprinting, methylation permanently regulates expression of either the maternal or paternal allele of particular genes at the start of development.
41
Who are some contributors of the discovery of DNA, and what were their contributions?
In 1928, Frederick Griffith discovered that bacteria can transfer genetic information. In the 1940s, Erwin Chargoff discovered that the number of purines (A, G) must equal the number of pyrimidines (T, C). In 1952, Hershey and Chase found that DNA is a genetic/hereditary material. In the early 1950s, Rosalind Franklin found that DAN has a helical structure with 2 strands and a sugar phosphate backbone. During the same time, Watson and Crick introduced the central dogma, which is the idea that genetic information flows as DNA is transcribed into RNA, which is then translated to make proteins.
42
What are the steps required to set-up the plasmid restriction digest?
A plasmid map is used to identify where the restriction enzymes are. The restriction sites identify where the enzymes are cut out and removed.
43
All cells follow the same central dogma. Explain what this is and how it can be used to explain how a gene from a human or sea anemone can be expressed in bacteria to make a new product.
The central dogma explains the order of protein production. First, DNA is transcribved into RNA, which is then translated into proteins. Because bacterial cells, sea anemone cells, and human cells make proteins the same way, this means that a gene from humans or sea anempne can be expressed in bacteria to make a product never before made in bacteria.
44
During ligation, which bonds form first: hydrogen bonds or covalent bonds? Why do both types of bonds need to form?
During ligation, hydrogen bonds form first. Hydrogen bonds first form between the unpaired bases at the sticky ends. Then, the ligase catalyzes the formation of covalent bonds between nucleotides that are adjacent to each other.
45
Explain the role of arabinose in the expression of the rfp gene in the pARA-R plasmid.
Arabinose is required in order for transcription of the rfp gene to occur. Arabinose is an activator protein that runs on the promoter, which then binds to RNA polymerase. Without arabinose, the promoter would not be turned on, RNA polymerase would not bind, and transcription of the rfp gene would not happen.
46
If a population experiences no migration, is very large, has no mutations, has random mating, and there is no selection, which of the following would you predict?
The make up of the population's gene pool will remain virtually the same as long as these conditions hold. The conditions described all contribute to genetic equilibrium, where it would be expected for initial gene frequencies to remain constant generation after generation.
47
What is a habitat?
the location or environment where an organism is most likely to be found/normally lives
48
A heterotroph is an organism that derives its nutritional requirements from complex organic substances. Are fungi heterotrophs?
Yes, fungi are heterotrophs that feed by absorptopn. Usually fungi secrete hydrolytic enzymes into their surroundings wich breaks down the complex molecules into smaller organic compouds that they can absorb.
49
What are homologous structures?
parts of the body that are similar in structure to other species' comparative parts. They prove as evidence that life on Earth has a common ancient ancestor that the diverse species have evolved from over time.
50
What are hybrid offspring?
offspring that result from an interspecific mating
51
How do you calculate logistic growth in a population?
dN/dt = rmaxN[(K-N)/K] where the carrying capacity is represented by K
52
Why might organisms migrate?
Organisms migrate, a regular long-distance change in location, for better living. Organisms migrate mainly to withstand weather changes, have access to better food, or to reproduce in a specific area
53
What is morphology?
the branch of biology that deals with the form of living organisms, and with relationships between their structures
54
When does population growth occur?
When mortality rates are greater than death rates
55
What are causes of mutations?
exposure to specific chemicals or radiation which cause the DNA to break down
56
What are sister groups?
two lineages sharing a common ancestor from which no other lineage has sprung sibilings
57
Interactions between organisms in a community can be commensalism, mutualism (or symbiosis), or parasitism. What type of interaction is barnacles and whales?
Commensalism because the barnacles get nutrients from floating plankton or other food materials around the whales, as well as transportation, and the whale is not harmed or benefited in any matter.
58
How does disruptive selection effect evolution?
the population goes against the mean, towards both extremes
59
What type of reproductive isolation has to do with physical barriers?
allopatric speciation. allopatric meaning "other country"
60
What is "cladistics"?
formilization of procedures that shows origins of trates
61
What is heterochromatin?
Genetic material that is highly condensed and not accessible for transcription of genes.
62
What is the function of helicase?
Helicase is an enzyme that untwist the double helix at replication forks, separating them into two parental strands and making them available as template strands.
63
What is the function of a histone protein?
Histone proteins are responsible for the first level of DNA packing in chromatin.
64
What is histone acetylation?
When acetyl groups are attached to lysines in histone tails, neutralizes the lysines' positive charges, and causing the histone tails to no longer bind to the neighboring nucleosomes.
65
What are introns?
Introns are noncoding segments of nucleic acid that lie between coding regions.
66
What is an inducer?
A small specific molecule that binds to a bacterial repressor protein and changes its shape so that it cannot bind to an operator.
67
What is the lagging strand?
The DNA strand synthesized by following the template strand in the direction away from the replication fork.
68
What is the leading strand?
The DNA strand synthesized continuously in the 5'-3' direction along a template strand.
69
Explain the role of ligase in DNA replication.
Ligase is used to join together the sugar phosphate backbones of all the Okazaki fragments into a continuous DNA strand.
70
What are missense mutations?
Substitutions that change one amino acid to another one.
71
What is the purpose of mRNA?
mRNA, or messenger RNA, carries a genetic message from the DNA to the protein-synthesizing machinery of the cell during translation.
72
What does a chi-squared test determine?
A Chi-squared test determines if there is a significant difference between the expected and observed data.
73
What is a nucleotide-pair substitution?
The replacement of one nucleotide and its partner with another pair of nucleotides.
74
What does the null hypothesis state?
The null hypothesis states that there is no statistically significant difference between the predicted and observed data.
75
What are nucleosomes?
The basic unit of DNA packing that makes up the beads in unfolded chromatin.
76
What are polyribosomes?
Strings of ribosomes that enable a cell to make many copies of a polypeptide very quickly.
77
What would happen if RNA polymerase malfunctioned?
Transcription would stop
78
What type of mutation would be the most potentially harmful?
A frameshift mutation, specifically one that is right after the start codon
79
Where does tRNA get the amino acids it brings to the ribosome from?
Aminoacyl tRNA synthetase attaches amino acids to tRNA from the cytosol
80
In the Hardy-Weinberg equations, what do p, q, p^2, 2pq, and q^2 represent?
p represents the frequency of the dominant allele (A); q represents the frequency of the recessive allele (a); q^2 represents the frequency of homozygous dominant individuals (AA); 2pq represents the frequency of heterozygous individuals (Aa); q^2 represents the frequency of homozygous recessive individuals in the population (aa)
81
Which leads to analogous structures, convergent or divergent evolution?
Convergent evolution
82
List four possible abiotic factors (in general).
possible answers include: space available, soil, climate/weather (wind, sun, humidity, precipitation), topography, availability/quality of water etc.
83
Why are sticky ends useful/important?
Specifically in cloning, they ensure the human DNA fragment is inserted into the plasmid in the right direction
84
What is the central dogma of biology?
DNA → RNA → protein
85
Why is a poly A tail added?
To protect against enzymatic degradation in the cytosol
86
What are the three modifications required for an RNA strand to leave the nucleus?
poly A tail, intron splicing, and a 5’ cap
87
Why is topoisomerase necessary?
DNA has a winding problem that is caused by the intertwined nature of its double-helical structure. During DNA replication and transcription, DNA can become overwound ahead of a replication fork, and topoisomerase can fix this
88
What do the two ribosomal subunits do?
The large subunit adds amino acids to the growing protein chain. The small subunit binds and decodes mRNA
89
On what basis does gel electrophoresis sort DNA molecules?
Their size
90
In DNA replication, which strand is fragmented, the leading or lagging?
Lagging
91
What is one example of a point mutation?
The mutation that causes sickle cell disease
92
Meiosis or Mitosis: Homologous chromosomes separate.
Meiosis
93
The sites of translation.
Ribosomes
94
What are 2 negative effects of a mutated p53 gene?
1) DNA can't be repaired 2) Cancer forms
95
What is the change in a single nucleotide pair of a gene called?
Point Mutation: if a point mutation occurs in a gamete or in a cell that gives rise to gametes, it may be transmitted to offspring and to a succession of future generations. If the mutation has an adverse effect on the phenotype of an organism, the mutant condition is referred to as a genetic disorder or hereditary disease. Ex: the genetic basis of sickle-cell disease has been traced to the mutation of a single nucleotide pair in the gene that encodes the B-globin polypeptide of hemoglobin. The change of a single nucleotide in the DNA's template strand leads to the production of an abnormal protein.
96
What is added to the 3' end of mRNA before it extits the nucleus?
Poly-A tail: an enzyme adds 50-250 more adenine nucleotides at the 3' end. The poly-A tail and the 5' cap share several important functions. First, they seem to facilitate the export of the mature mRNA from the nucleus. Second, they help protect the mRNA from degradation by hydrolyic enzymes. THird, they help ribosomes attach the the 5' end of the mRNA once the mRNA reaches the cytoplasm
97
What is the best way to produce an exponentially growing population of identical DNA molecules when the source of DNA is scanty or impure?
The Polymerase Chain Reaction is quicker and more selective than DNA cloning. In the PCR procedure, a three-step cycle brings about a chain reaction that produces an exponentially growing population of DNA molecules. During each cycle, the reaction mixture is heated to denature (separate) the DNA strands and then cooled to allow annealing (hydrogen bonding) of short, single-stranded DNA primers complementary to sequences on opposite strands at each end of the target sequence; finally, a heat stable DNA polymerase extends the primers in the 5'-3' direction.
98
What are DNA molecules formed when segments of DNA from two different species are combined in vitro called?
Recombinant DNA: to clone pieces of DNA in the laboratory, researchers first obtain a plasmid (originally isolated from a bacterical cell and genetically engineered for efficient cloning) and insert DNA from another source ("foreign" DNA) into it. The resulting plasmid is now a recombinant DNA molecule. The plasmid is then returned to a bacterial cell, producing a recombinant bacterium. This single cell reproduces through repeated cell divisions to form a clone of cells, a population of geneticaly identical cells.
99
What is at the end of a replication bubble?
Replication Fork: a Y-shaped region where the parental strands of DNA are being unwound and new strands are being synthesized
100
What can inhibit gene transcription?
Repressor: a protein that inhibits gene transcription. In prokaryotes, repressors bind to the DNA in or near the promoter. In eukaryotes, repressors may bind to control elements within enhancers, to activators, or to other proteins in a way that blocks activators from binding to DNA
101
What gene is involved in controlling the expression of one or more other genes?
Regulator Genes: In prokaryotes, regulator genes often code for repressor proteins which bind to operators or promoters, preventing RNA poymerase from transcribing RNA. Other regulatory genes code for activator proteins. An activator binds to a site on the DNA molecule and causes an increase in transcription of a nearby gene.
102
What cuts up phage DNA after it successfully enters a bacterium?
Restriction Enzymes: When phage DNA successfully enters a bacterium, the DNA often is identified as foreign and cut up by cellular enzymes called restriction enzymes, which are so named because their activity restricts the ability of the phage to infect the bacterium. The bacterial cell's own DNA is methylated in a way that prevents attackby its own restriction enzymes. But just as natural selection favors bacteria with mutant receptors or effective restriction enzymes, it also favors phage mutants that can bind the altered receptors or are resistant to particular restriction enzymes. Thus, the parasite-host relationship is in constant evolutionary flux.
103
Where does translation take place?
Ribosomes: complex particles that facilitate the ordlerly linking of amino acids into polypeptide chains. Ribosomes are the sites at which the genetic code is actually read by a cell. Ribosomes are themselves composed of a complex of proteins and specialized RNA molecules called ribosomal RNA (rRNA). During translation, ribosomes move along an mRNA strand, and with the help of proteins called initiation factors, elongation factors, and release factors, they assemble the sequence of amino acids indicated by the mRNA, thereby forming a protein. In order for this assembly to occcur, however, the ribosomes must be surrounded by small but critical molecules called transfer RNA (tRNA). Each tRNA molecule consists of two distinct ends, one of which binds to a specific amino acid, and the other which binds to a specific codon in the mRNA sequence because it carries a series of nucleotids called an anticodon. In this way, tRNA functions as an adapter between the genetic message and the protein product.
104
What enzyme separates the two DNA strands and joins together RNA nucleotides?
RNA polymerase: pries the two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand, thus elongating the RNA polynucleotide. Like the DNA polymerases that function in DNA replication, RNA polymerases can assemble a polynucleotide only in the 5'-3' direction. Unlike DNA polymerases, however, RNA polymjerases are able to start a chain from scratch and don't need a primer. The DNA sequence where RNA polymerase attaches and initiates transcription is known as the promoter. In bacteria, the RNA polymerase itself specifically recognizes and binds to the promoter. In eukaryotes, a collection of proteins called transcription factors mediate the binding of RNA polymerase and the inititation of transcription.
105
What was the model of DNA replication discovered by Watson and Crick in 1953?
Semi-Conservative: Watson and Crick's model predicts that when a double helix replicates, each of the two daughter molecules will have one old strand, from the parental molecule, and one newly made strand. The semiconservative model can be distinguished from a conservatite model of replication, in which the two parental strands somehow come back together after the process.
106
What kind of mutation has no conservable effect on the phenotype?
Silent Mutation: Some nucelotide-pair substitutions have no effect on ther encoded protein, owing to the redundancy of the genetic code. For example, if 3'-CCG-5' on the template strand mutated to 3'-CCA-5', the mRNA codon that used to be GGC would become GGU, but a glycine would still be inserted at the proper location in the protein. In other words, a change in a nucleotide pair may transform one codon into another that is translated into the same amino acid.
107
What is assembled from snRNPs and protein complexes?
Spliceosome: several different snRNPs join with additional proteins to form an even larger assembly called a spliceosome, which is almost as big as a ribosome. The spliceosome interacts with certain sites along an intron, releasing the intron, which is rapidly degraded, and joining togther the two exons that flanked the intron. It turns out that snRNAs catalyze these processes as well as participating in spliceosome assembly and splice site recognition.
108
What is the first codon of a messenger RNA transcript that is translated by a ribosome?
Start Codon: the start codon is the first codon of a mRNA transcript translated by a ribosome and always codes for methionine in eukaryote. THe most common start codon is AUG.
109
What is the nucleotide triplet within messenger RNA that signals a termination of translation called?
Stop Codon: elongation continues until a stop codon in the mRNA reaches the A site of the ribosome. The nucleotide base triplets UAG, UAA, and UGA do not code for amino acids but instead act as signals to stop translation.
